The idea of implementing a more archipelago-like situation between ocean continents seems ideal for making ocean travel more interesting and alive.
A couple additional water biomes that could act as replacements for shallows, or potentially even creating a new “medium water depth” could solve this problem. Presumably a mid-tier depth would cause damage to a boat less frequently than deep water – or biomes like rocky shoal and coral reef could potentially ONLY damage bigger boats due to the potential for hitting rocks with the hull.
Biomes such as seaweed beds,

seagrass meadows,

coral reefs,

and rocky shoals

could be randomly strewn around islands and act as additional diversifying areas for water foraging and critter spawning. I will make another thread for flora and fauna suggestions so this doesn't become too much of a grab-bag.