Welcome to the forum!
Unfortunately, I can't think of any way to avoid those problems.....assuming you're drawing them from scratch yourself. And fixing them is just what you're already doing -- manually, and one at a time.
As long as I've been using Inkscape (just as a hobby, for over 10 years) these have been accepted problems with Inkscape. You know "that's just the way it is". But if they are causing significant problems for digital cutters, maybe they should be considered more serious, and get a higher priority for fixing?
But if you aren't drawing them yourself, perhaps we can investigate how your drawings are being created? Like if you're using Trace Bitmap, some adjustment of settings might help prevent the double nodes somewhat.