No problem leaving the documentation number there. In fact, I think you should leave it in case someone down the road wants to redocument it. Removing the number may raise questions about the boat's lineage, whether it was stolen at some point, etc. There is also no problem with having a boat that has been removed from documentation. In fact, when a documented boat is sold, it is automatically removed from documentation and doesn't get returned until the new owner files to do so. Normally that's a back-to-back process, but I found this out the hard way when I thought filing the USCG Bill of Sale would also switch the documentation to my name. It didn't.
I've done the documentation paperwork twice myself, and paid someone the third time. If you have time, are detail-oriented, and don't mind doing some research, it can easily be done yourself. But you are still likely to make a mistake or two that will slow the process. If you are in a hurry or are not detail-oriented, then using a documentation agent is money well spent.
My first time I got it all right.
My second time I made a mistake that slowed things a bit, but I had plenty of time so no big deal.
The third time I hired someone because I needed to get it through quickly