1. Multiple small notebooks. I love ~50pg, 5"x7" lined notebooks. They're cheap, and portable. Just get one for each project.
2. I usually allow myself 1-2 extra pages for longer thoughts or things that will require follow-up. That almost always works.
3. Indexes. Set aside 20pgs at the front (or back) for a table of contents. I do this with my longer notebooks (~200pgs) and I never have trouble finding things. If you need to continue a section later on call it "Project X (cont.)"
I feel like #3 is something that generations before us knew implicitly that we've forgotten.
[edit: grammar]
[Edit: Addendum]
Also, always date your entries. That helps a lot.
If the material is something I particularly need to remember, I can shift it to an actual reference document which contains all the most essential details.
Highly recommend.
I can't use any other type of notebook more or less for the same reason as you, and this has made me stop worrying too much about writing stuff "the wrong way" or having the notebook become too thin because I remove sheets.
So I just start writing about a "topic" on its own blank sheet, and then I periodically move stuff around when I need more pages. If I know I will write/draw a lot about a topic (e.g. a project I'm still brainstorming), I usually leave a few blank sheets between this and the next topic.
Any unused blank pages can be shuffled around anytime. I like to move "quick reference" stuff to the beginning.
The notebook always has roughly the same amount of sheets because even if I remove a few, I can add more in their place.
If you go specifically for MUJI and want to try this out, the normal way would be to use their "loose leaf cover", but you'll only be able to fit around 80 sheets or so. If you want something more chonky, you can use their kraft or polypropylene binders as "cover" and just use that as notebook. I'm literally doing that, and it seems to be an expected use, because each loose leaf package has a suspiciously convenient amount of sheets to conveniently fit one binder.