There are 2 ways to think about this assuming that you are talking about a gap under the floor that connects the bilge with the space under the seats. Here is how my salon floor looked on my Starwind 27 as I was replacing my floor.
See those teak rails under the cushions? The fiberglass liner sealed the void under the seat from the bilge. I thought about punching a few limber holes under the floor but decided not to.
You can seal this area up and prevent bilge water vapor from permeating the space under the seats. You will have the occasional water collection in those spaces if you have deck leaks. This might be easier said than accomplished, so think it thru.
Or, you can let that space drain and leave it open to the bilge water contamination.
I much prefer that it be closed. The bilge tends to be nastier and more pervasive than any water that might collect in those spaces under the seats. Sure, I mopped up under the seats occasionally, but there was nothing fetid about it. It was clean even if it was a bit of a nuisance.
Few people have 30-40 year old boats that are perfect. I certainly didn't. You can still sail perfectly well even if there are a few warts. Some people act as if any deviation from perfectly clean, sanitary and structurally perfect is the basis for a negative value. I did not find that to be the case. And if you read enough posts in here, you realize that there are multitudes of people whom are willing to jump all over just about any complete hunk of junk if they think they are getting a deal.
Take care of those warts to the best of your ability and go sailing. No boat is perfect, but there are plenty that are worthy of enjoyment despite the imperfections. I think I would attempt to seal off that bilge and then strive to eliminate any vexing leaks that may contribute to a little water under the seats from time to time.