i have no previous experience whatsoever with things like this but:
check if your heel has them too, if not, leave it on otherwise your boot will be tilted in the binding and might not eject properly.
second: if you do remove the baseplates i suggest putting inserts, helicoils in the holes and trimming the screws to proper length (they'll be (plate diameter) too long)
The helicoils are because you've unscrewed a screw in your wooden ski, making the thread going easier but also making it easier for the screw to pop out or water to come in and start rotting your core. If you don't wanna use helicoils and still feel confident about the holes, be sure to fill the hole with wood glue, then insert the screws (this keeps water from getting in, it doesnt glue your screw ! it just keeps water out)
Oh and if the plates came in with your bindings and they're not a shop mod then they might be crucial to your binding design, so check that out first...