Be have our original everything, but we've also needed them. If you've ever had a child in another country and needed to establish multiple citizenships then you know what kind of shenanigans it can be.
Boat paperwork itself has been a non issue, but when you deal with consulates, local ministries, and embassies often the original is the only thing that will suffice when it comes to the paperwork of the crew. Ditto for immunization records.
Regarding USCG documentation
I'd recommend getting a double-sided color photocopy (or 5) made at a Kinkos or whatever in the US before you leave. They're really high quality and look almost exactly like the originals. In fact I've confused the copies for the originals, the only way I can tell is that the original has fold marks from when it came in the mail.
When on passage
we put our passports in a ziplock and in the ditch bag.