question

Do you need to physically decouple the batteries? Or software limit charging/discharging or turn off the whole system?

Ideally you should have a dual pole isolator switch for the PV (solar) panels, and also an isolator switch (and fuse) for the battery +ve connection. When disconnecting, always disconnect the solar panels first (and reconnect last when putting it back together). You do have MC4 connectors so you can disconnect those at the MPPT (there is a simple tool you can get for releasing locking tabs on MC4 connectors).

Don't leave AGM batteries uncharged. Top them up at least monthly, or you're going to be buying new ones. Don't disconnect MC4 connectors under load, they're not designed for it.

Regs here demand battery Isolators in a marked location.

Ideally, your boat already provides isolating switches for all the PV panels and the battery to disconnect them. In Germany (and most other countries?) there are local regulations that even demand them. So you can simply switch off the isolating switches.

However, I also know that most electrical systems on non-commercial leisure boats are not installed by licensed electricians, but the the boat owners themselves and I have rarely seen installations which fully comply with regulations. So chances are that these switches are actually missing.

If they are missing then I recommend to add them if you are going to work on the boat during winter storage anyway.

Disconnecting only the plus terminal might be insufficient. That is why all isolating switches disconnect both poles. If there is no isolating switch and you have to disconnect the battery manually, please be extremely careful and start with the minus terminal. On most boats the electric system is minus grounded, i.e. the minus terminal has an electrical connection to ground and all other metal objects on the boat, namely the engine housing, drive shaft, anchor winch, etc. If you disconnect the plus terminal first and accidentally touch any metal object with your tools such that you create an unintended connection between the plus pole and the ground while you are working on it, you have a full short-circuit running through your tool.

As always the truth is much more complicated. The relevant sources on are EN ISO 13297 Small craft - Electrical systems - Alternating and direct current installations on the EU level and VDE 0129 Part 507 Electrical installation in ships - Pleasure craft on the German level. If you are not located in Germany the latter is irrelevant for you. But maybe there are other local regulations for your jurisdiction.

I own a copy of both regulations. Of course, each of them refers to further regulations.

Disclaimer: I only started my own investigations a couple of weeks ago. Normally, I do "standard" electrical installations in non-commercial buildings. Wiring a yacht is a private side project for a family member. So chances are that I don't have the complete picture yet. However, I was annoyed that apparently nobody was able to provide substantiated directions, so I read the regulations myself. (Besides I am a big fan of regulations. :D)

First, I would like to direct you to one of my own questions from some weeks ago: Battery switch vs. yacht main switch: Must they be the same?. I was wondering whether one really needs to disconnect the battery if one leaves the yacht and how one is supposed to charge the battery during time of absence. The accepted answer to that question is perfectly right and I double checked with the original text of the regulation which I did not know back then but which I have read in the meantime.

On the EU level: The EN ISO 13297 requires an isolation switch after the battery, but makes a series of exceptions. For example, chargers may remain connected to the battery in order to allow charging in time of absence. If one takes everything together one could have put it down in less words: Basically there must be a switch which separates the battery and chargers on the one side from the loads on the other side.

Unfortunately, the regulation calls this switch the "battery switch". IMHO, a much better term would have been "load main switch", because that is the true purpose of that switch. (Probably that is source of so much confusion). In the following, I will use the term "load main switch". That term becomes important when compared with German VDE regulations.

One important aspect is the number of poles: In a minus-grounded DC system, the "load main switch" must only disconnect the plus conductor. That is a safety measure and ensures that the loads still remain grounded. Only if you have a DC installation where the minus conductor is separated from the PE conductor, then the "load main switch" must disconnect the plus and minus conductor (of course the "PE" remains continuous). However, I believe the minus-grounded DC system is the more usual use case.

The "load main switch" is the switch which you have to put into OFF position, when you leave the boat.

Everything on the battery/charger side which remains connected must be individually protected by protective devices (i.e. fuses or MCBs). Note this does not refer to connections between the PV panel and the input of the MPPT, but the output of the MPPT and the other chargers and battery. If one MPPT, charger, whatever fails and causes an over-current, the rest is protected.

This answers one of your question: You don't need to cover your PV panels when you leave the boat. Au contraire: You can even use them to charge the battery (or keep it in float). You only need to disconnect the loads.

Now let's turn to specific German regulations. I don't know if they apply to you, but usually other EU countries have identical regulations. Besides the aforementioned "load main switch" due to EU regulations (which, I am repeating myself, is confusingly called a battery switch), in Germany, the VDE requires a real battery switch. That battery switch must always be a two-pole switch and disconnect both poles of the battery. This switch sits between the battery and chargers. However, you only need this switch for maintenance work on the battery, e.g. if you replace a broken battery by a spare one. You don't need to operate that battery switch under normal conditions, in particular you don't need to switch it off when you leave the boat.

One more word on grounding: In a minus-grounded DC net, the minus pole must be grounded after the battery switch. Again, the rest of the system must remain grounded for safety reasons, if you switch off the battery switch in order to completely isolate the battery for maintenance work. In Germany this rule is called "Durchgängigkeit des Schutzleiters" ("continuity of the PE conductor").

Now let's turn to your last question regarding isolation switches and protective devices between the PV panel and the input side of the MPPT. (Here I am less certain as I still fear to not found and read all regulations.) But as far as I see it, the following holds. On the EU level there is no regulation concerning boats. (There is a rule which requires an isolation switch for fixed installed PV panel on building roofs, though.) In Germany, there must be a protective device (i.e. a fuse or MCB) in two cases:

1. The short-circuit current I_sc of the PV panel is higher than the rating of the cable or higher than the allowed input current of the MPPT.
2. You have a parallel connection of two or more strings of PV panels which feed the same MPPT input.

Case 1 should not occur as this implies a planning error. It essentially means that your PV panel is too powerful for the cable or the MPPT and that you won't be able to use all available power. (Moreover, the fuse will blow or the MCB will trip on a sunny day.) In case 2, each string must be protected separately, i.e. before the strings run together. The protective device must be rated high enough such that the short-circuit current of the protected string can safely pass, but low enough such that the string is protected against destructive reverse current from the other strings.

However, I assume that the typical installation on a (small) boat is a single PV panel for one MPPT. It appears to me that in that specific case, i.e. a one-to-one correspondence, there is no regulatory obligation to have a isolation switch or protective device between the PV panel and the input of the MPPT.

PS: If I find the time, I will draw a diagram which illustrates all these rules.