the wave problem can only be avoided by digging inland with the pickaxe or finding a natural BAY area as in this the waves arent as high. right at oceansite there is just nothing you can do againist waves flooding in if the structure isnt high enough up above the biggest waves youll get flooded. dont build the mainbase too close to oceansite or raise ground level to maximum first and see if it stays above the waves during a storm.

for the ships a bay/river/lake access is the only way to prevent boats from bouncing. a open sea harbor just doesnt work during a storm. boats will jump.

as for the spawns. make sure you have 100% area covered. workbenches show the radius at which they block spawns. if a bench is destroyed spawns become possible again. if there is even a small spot that isnt covered mobs can spawn there and annoy you.

make sure its not a mod causeing this if you run any.

its pretty simple to avoid spawns in the base otherwise (aside bats. they can spawn anywhere that isnt a shelter area even on the ocean)