Two things I'd suggest. The first is to cover the boat. Crimes of opportunity are the easiest to deter and an open boat at night is an easy target. You could add some sort of warning device to the cover so if a bad guy does attempt to remove it, he is then giving up the stealth that he was also relying on.  Second, either keep your electronics in the Pilot with you, or lock them in one of your lockers.  If you don't have lockable storage, put everything inside with you.  I hang my rods from the ceiling of my Pilot and there is enough room on the floor and front seats for most of your other gear.

On my Pilot, the rear window can be opened. If yours can be, leave it closed but unlatched. A quick push and you can exit quickly, or just point your Sig and chase the perp away.  I wouldn't advise shooting as I don't know many states that would condone it.

I've slept in the back of my truck at a boat ramp parking lot several times .