I don't think this is the first time this has every been done by dealers. I would expect if you purchased any new boat from dealer inventory there is a good chance that it has been demo'd without the hour meters hooked up.
I would go to another dealer that has the computer scan tool. From what I understand it can tell you exactly how many hours are on the engines and how they were run in terms of max RPM.
If this checked out OK I would not worry about it.