Water Holes in the Floor

I'm assuming that at some point, someone has put holes in their floor to let water out after you get in too deep. Should I just drill a hole or maybe cut knock out the plastic pieces and leave the hole like it is, or should I put some kind of valve or cover over them that I can open when I need to?

At the moment I've got some kind of leak on the passenger side that allows water to come when it rains, so I've got to do something anyway. I can't find any problem with the door seal, so I'm thinking that the water might be coming in through the vents.

Actually, I just pulled out all of my carpet and found 9 water drain holes. 2 under each front seat, 2 on the rear floor, one under the back seat, and 4 in the hatch. Unfortunately you have to take out your carpet to use them. But who wants carpet that you have to vacume, using a hose is so much easier.