Is there some way to hide all topics within a category from all feeds (recent, popular, new, the digest)?
I need the topics to be accessible (and usable) to all users directly, but not searchable or showing up at random.
I am planning on having several plugins coded by freelancers, Is there anything in the core, or otherwise, that would prevent me from removing the categories from the home page and placing them into an offcanvas sidebar?
Not really, NodeBB is pretty flexible with this. Your plugin could just expose a new route as "home page", and put all the categories in a sidebar in your theme.
Awesome. I chose Nodebb for flexibility; become the forum/CMS that I need. Nodebb never ceases to surpass expectations.