I have a couple of holes from the previous owner, who use a skrew too long, and made a small hole.

I was going to repair with 3m 5200 Marine silicone. One person suggested I put a wood dowel in as well.

(Small hole 1/8 " or 3 mm)

Is the hole through the hull below the floor or where is it at? Although I think the 5200 would work I would use something more permanent like Marine Tex. http://www.marinetex.com/