1)  If the missing wood is still there, glue it back where it belongs, if not then square up the hole and put in new wood

2)  Sand down the glass on both sides of the hole to the wood and smooth out new wood.

3)add new glass extending at least 2 inches all the way around on both sides with epoxy and fill coats.  Do a little feathered sanding till it is smooth.

4) re varnish outside

5) Go Paddle

If you do a little grain matching, and some careful sanding, only you will ever know the patch is there

KK

My kayak came off my roofrack and landed in the road. Being 3mm plywood it was easy to hole. Since I had all the broken pieces I merely epoxied them in place with a little jacking from behind to make the piece curve like the rest of the hull. There was a little taper on the edges of the broken area to make a satisfactory glue joint. Then I glueed a piece of 9 oz. glass behind it.