The primary advantage of Supercaps is that they work in all temperatures, have nearly infinite life, and weigh very little compared to a battery. They do have a self-discharge problem but can be charged from dead to operational in a few minutes.
They make sense in a hybrid car, for an example. When you slow down, the inertia drives a generator that charges the supercap up. When you accelerate, you drain the supercap, so you get the effect of having a more powerful engine because the engine and the generator/motor are pulling the car up to speed. They weigh very little, compared to even Lithium Ion batteries and far less than lead-acid batteries.
Does it make sense in a boat? No, since it would not replace your house bank. It might replace your starting bank, and be charged off the house bank. It certainly would make wiring simpler, since all you ever need to charge is the house bank.