It depends on how large they are and whether they go through the cabinet. If they are small enough you can just put screws in them if bigger wood dowels. Are you sure they aren't ports though?
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If they penetrate all the way into the cabinet void they will have some affect on the sound, particularly if they are sealed (acoustic suspension) design. If they are ported, its less of a concern. Silicone is a good idea for a fix. I assume that you can tell the difference between a port (which typically is a flared plastic "vent" extending well into the cabinet, usually diameter on the order of inches, not 1/16ths. A ported speaker is also called a reflex or bass-reflex design.