I would get some west epoxy, colloidal silca(thickener), fill it in and sand it smooth. make sure to sand and clean first.
If you want to make the bottom harder and slicker. You can get graphite filler, mix up a batch of epoxy and paint the graphite filled epoxy on. It makes for a very hard, slick surface. It will add a little weight to the boat, but not enough to notice. It will cure to a black color.
Canoe Pack Liner
The Kayak Wing
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