Sounds like you have just acquired someone else's pain. There should never be a need for the business end of a screw to puncture the outer skin of the boat. This is a place where she's leaking.
Find out what's being screwed to the bottom of the boat and remove it from the inside (back out the screws) A marine sealant or adhesive could provide a temporary fix, but the hole(s) should be 'glassed in properly.
I've seen 3M 5200 fix a world of hurts, but I'll bet you have other issues with this boat, seeing that the bone head that owned her before saw fit to drive screws that way, she'll surly have more bone headed stuff to deal with.
Good Luck,