Why are the coins in the sewers of Super Mario Sunshine question marks?
Solution 1:
This isn't specific to coins - any items in the sewers that you can't see are question marks, and you'll have to judge by the sound (among other things) to determine what you pick up.
Coins are by far the most common, but you can also run into 1-UP mushrooms.
Solution 2:
It is because the camera can't see them. Simple as that. They added this so you can still see what is going on.