2016 SE and using plural battery, Safe to assume the boat has a master battery switch. Off should disconnect all loads from the battery except maybe the auto bilge. If this case, no need to disconnect any additional cables as that would be redundant.

I prefer to not pull batteries. A fully charged battery with no parasitic loads should last a winter layup. If the boat has an on-board and the storage spot has access to a 110 outlet, then use the charger with the batteries in place.