Ok, if this acid is burning through Merry's hull at a decent rate, how the hell are there skulls not complete mush?

Wood decays faster than calcium?

Depending on the acid, it varies. Given this is one piece, who knows what type of acid a whale the size of an island has, but given how it's apparently ineffective against Iron/steel, it's not all powerful.

Correct. Human stomach acid is actually one of the more potent, being able to dissolve a crazy number of things that many other members of the animal kingdom simply can't.

For some specific examples, owls regularly regurgitate 'owl pellets' which are basically the hair and bones of the rodents they eat, which their stomach can't process. Also, cutting open a shark's stomach can sometimes be like opening a treasure chest of random things because they will frequently eat man-made items they can't digest at all.

For the record, GM said "1d8+4, or 2D8+8 if you're near the walls" on page 1364

If dnd bones were digestible, there wouldn't be skeletons in gelatinous cubes and that'd be a shame.

Truly the most important reason for bones to not be digested.

In my experience, usually the bones in gelatinous cubes are less actual bone and more crystalline carvings in the shape of bones.