You might want to try a Dremel tool with a cut-off wheel. Slowly (so as not to get too hot and burn the fibreglass) cut a screwdriver slot in the exposed end of the screw. If you cut a little into the gelcoat no biggie. Those are smaaaal screws to drill out for an easyout!
My Mod 2 is so covered with gelcoat cracks, it would take a month to repair them all. Even as they are, it's hard to see them from more than a couple feet away. Unless you can easily flex them open, which indicates the underlying layers are cracked or broken, I wouldn't bother. But maybe that's just me.