Sealing all sides of the wooden keel piece before installation. The canoe industry is about the only branch of boatbuilding where pieces of raw wood are frequently placed up against other surfaces without being properly sealed or bedded, and then simply varnished on the part that still shows. That's not really a particularly sound practice for building boats and water is likely to eventually get in there and start soaking into the raw wood. The result degrades the piece structurally, and will also often eventually lift the varnish off of the exposed portion.
If you have (or had) to cut down into the glass with a Forstner bit, just to get to the screw heads, and then you take out the screws (and the volume their heads used to occupy in the holes) then the remaining fiberglass may be kind of thin in those spots. New holes through all of the original fiberglass might be stronger, as well as smaller in diameter, easier to seal, etc. but it's hard to say for sure without actually seeing the boat. I still think the strongest approach would probably be to use a Dremel and a cut-off wheel to cut the screws off flush with the bottom, without messing up the glass inside and then mount the new keel with new screws, sealer and finish washers in new holes from the inside.