Had been many years since the mutiny, so I guess any damage may have been repaired.
His story about repairing meteor damage appeared to be plausible to the Palomino
crew - I think Holland distrusted the man rather than his cover story. So if they believe disabling damage may be repaired in that amount of time, fixing laser holes in the walls should be a doddle.
For all we know though, the reason that Reinhart was so insistant on no "unescorted excursions" is there may have been some areas of the ship that still showed such evidence. Perhaps some crew managed to seal themselves off, and Reinhart just let them starve to death, or decompressed the area. If it was an area not vital to the operation of the ship or his experiments, I doubt he'd have given a second thought to regaining access to it or fixing it up.