Really curious how there’s that many sections missing. Probably lost to time why…

I think adding relations for longer waterways is totally fine. It’s very common and makes a nice single place to grab the whole thing.

Features with that FCode should be marked as intermittent and, given the grography of OK, I’m not surprised at the large number of ways. In case you haven’t seen this, the wiki has a page talking generally about NHD imports that mentions this. There may be other FCodes that could use some scrutiny while you’re there.