Prevent Category Pages from Generating
If you really want to prevent the URLs from existing at all, you could probably unset the paths using a hook_menu_alter. I would be careful with that though, as it might have unforseen consequences. The creating module may in some way depend on the paths existance.

I don't know where the category paths comes from but I guess the answer will be the same as for the taxonomy ones.

My solution would be to take over the URL with Page manager, and simply pass the user a redirect to the front page. (Or a 404, if you prefer).
Note that I'm talking about "Page manager" in Ctools, not Panels. The two modules are often confused and their names interchanged.