It really depends... in my boat, there really isn't any place for water sitting in those cutouts to go. I'd spray some cleaner down there, blast it with a bit of clean water and vacuum or mop up the water. That should let you get a better look -- even if it requires putting your smartphone an a selfie stick -- at what's in there. It's not uncommon for organic stuff to get caught in those and get nasty, if there's water sitting in the bilge.
The bilge is designed to collect water, so having some back there by itself should not be a big problem. If there was a lot of water, and if the water was in contact with any fiberglass-covered wood structures, then you might want to look to see if there are cracks or holes where the water might have infiltrated the wood.