I DIDN'T RUIN MY BOAT, DID I?

I recently went outside to inspect my winterized '05 Wakesetter after a rain storm, and discovered something that alarmed me- my boat was leaking! It was leaking from what I identified as the v-drive shaft opening. I guess what had happened was that rain water had entered through that hole that some covers have on the top. Then obviously, it had dripped down to the hull area. Is there a chance that I screwed up my boat, either that particular seal or the pump/instrumentation that's down there? I know that a few of the nights that the water would have been in there it was near freezing (27 to 32 degrees). Lemme know guys, thanks.

BTW, while I'm on the subject, why does my cover have that hole on it (it's located about 2/3 of the way back from the nose and is about 4 inches wide). It appears to be serving no function (it doesn't allow a ski pole to pass through or anything, because I have a v-drive) and doesn't really seem necessary. Can I just sew it shut?