Whilst I can see value in OSM mapping historical features, it's really not designed for it at the moment. I'd suggest that the sections that are entirely unrecognisable as a canal on the ground (totally filled in) shouldn't be tagged as canal at all. If there's still a footpath alongside, maybe that should be somehow tagged as a former towpath?

Having read the proposal for an abandoned tag, it sounds like the difference between that and disused would be quite subtle. If you're talking about the Wilts and Berks canal, there's a group of people aiming to eventually restore it to a usable condition, so it's not entirely abandoned. Neither is it "merely" disused, as I think you'd have a job getting any kind of boat through most of it.

Given that abandoned is just a proposal, I'd be tempted to just tag everywhere that still looks a bit like a canal as disused, and delete the parts that have been filled in or replaced by roads/houses.

JOSM's validator plugin can spot duplicate nodes. I discovered a whole bunch of roads on top of each other around Didcot when I tried it a few months back.