A few things come to mind.
I assume that the rotors are sticking to the pads as opposed to the breaks getting stuck in the 'applied' state.
First thing is to make sure the breaks are not activated when stored. Make sure that the last motion you make when storing is forward so that the actuator isn't compressed.(for surge brakes)
Corrosion on the disks is common and unavoidable if the disks get wet ( stainless disks are different), so the goal is to try and get the pads off of the disks. If you have floating calipers ( you may not) make sure the pins are clean and lubed with the appropriate lubricant. Make sure the caliper pistons move in their cylinder.
When you store the boat, after all is set and blocked, see if you can manually retract the pads by applying some pressure between the pad and the disk. Just a little space will help. You may have to open the bleeder valve when retracting the pad. Just be sure not to let air into the system.
One final though is that the pistons may be stuck caused by corrosion the the caliper. This really can't be fixed except by replacement and can be caused my moisture in the brake fluid. It is a good idea to change the fluid every couple of seasons. Look in the fluid reservoir for signs of moisture; creamy look, foam, rust, etc.
Good luck