Those are the ports for an in-floor cleaning system. Do you have wall returns? If not how are you going to get filtered water back to the pool. Some IFCS also had one or two wall returns in the system. You should have at least two for good circulation. If you don't have at least two, two or three of those ports could be converted to actual floor returns and the rest filled as below. Takes a little work, but I've done it successfully.
If you have wall returns, then yes, use a roto-hammer or small jack-hammer and cut them out, fill with hydraulic cement so that they can be plastered over with the rest of the re-plaster. I wouldn't trust just filling and plastering over the plastic.
This is a true floor return, that center cone threads into the glued and plastered-in receiver:
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