I believe what you are referring to is floatation foam which is required by Law for this size of boat. Sorry not familiar with this boat however these holes can be glassed over and lots of builders do so.
Is there some type of flange or screw holes for the plugs? Not sure why anyone would remove them.
1997 2400 SCR
5.7 Vortec / Bravo 2
Interesting. Do you have a pic?? I've seen MANY foam cored hulls. I don't ever remember seeing plugs in the hull. I wasn't aware the foam hulls were injected. I was under the impression they were sandwiched together.