They should be in port if the maintenance is low, as they can't defend themselves.
This is wrong.
0% naval maintenance means 0
bonus morale and -50% light ship trade power.
100% naval maintenance means +2.0
bonus morale.
While it is strongly advisable to fight naval wars at 100% naval maintenance, running at minimal maintenance does not mean that a fleet is defenseless and doomed in combat unless its base morale is zero. The earlier in the game you are, the lower base morale your fleets will have and the more important the bonus morale from running high maintenance will be, but just as with armies, navies will fight and do their level best to win regardless of maintenance settings. Select the level of maintenance that strikes a balance between what morale you find you need at minimum in battle in case of a surprise war, what level of trade power from ships you feel you need, and the expenses you have to pay each month and you are set.
(Of course, if a significant amount of your income comes from trade due to your use of light ships, you have a very good reason for running 100% maintenance at all times, and if you do not use light ships for trade at all your navy should probably stay in port, but that is another matter.)