Figured out how to do this. Create a new category and disable it. You can still use its products in trading packs, and they don't appear in the shop.
I'd really like to clean up the 'purchases' interface though. Ideally products need to stack here, and I can't imagine it would be too difficult. Just get it to search for any more products owned with the same name, and if it finds them hide all but one and put a number next to it. I'd absolutely love this. This add-on has HUGE potential if it's given the right attention.