The holes aren't a big deal. My fiberglass boat used to have poly, and then all the holes were glassed over when the hull bottom was re-done WITHOUT poly. Something cracked up and one of the holes totally opened up. 1/4" hole you could see daylight thru when you did a banking turn. It made a little fountain in the bottom of the boat, about 2 or 3 inches tall. Water came in at such a slow rate, it took forever for it to fill up enough so the bilge pump could pump it out. I was scared at first when I saw it, and then realized it may have been there for several trips out. So I shared your same fear about holes in a hull, and discovered it to be a real yawner when it actually happened.
I pulled the boat up on a log so I could get at the bottom, I ended up just putting a pan-head screw w/rubber washer in there. Problem solved. Next time I've got the boat on the trailer, I'll glass it. (If I even bother to remember!)
matt.