I wouldn't use wood dowels, unless that's all you can find, but there are some fiberglass dowels out there about the right size used as rebar for decorative cement blocks that work real well...just a Thought
I dunno...<br /><br />The whole dog-gone transom is most likely plywood sandwiched in glass. The dowels will only act as a solid to backfill the marine-tex against. Should water get past the marine-tex...rotting dowels will the least of your worries. Also, you'll probably have little trouble finding a wooden dowel that's the proper size of the existing hole.
wooden dowels method done exactly like PURSUIT said is the best way.. water WILL NOT get past epoxy !! if the hole is to small for the dowel,,, drill it out to the rite size... it's that simple...