You need to use the global visibility (monitor icon) instead of the eye icon to hide objects in instanced collections. Or go to Object properties > Visibility > Uncheck "Show in ... Viewports"
If you don't see the Monitor icon in the outliner, please refer to : Where are the outliner toggles in 2.8?
One of the users is the mesh instance itself of course.
The other is a custom property on the object that refers to the mesh instance named "lod_original". Look for it in the Properties editor. If you delete it, the user count drops to 1.
(One way to find this out: note that linked-duplicating the object increased the count by 2, so the second ...
Yes, I'm aware that this question is 9 months old, and I assume that the OP has either figured out the problem or moved on, but since I was having the exact same problem and I was finally able to come up with a solution (through a lot of struggle) , I'm going to post an answer for future reference. I had better luck understanding the problem with ...
The right thing to do is going into the header menu > Object > Relations > Make Single User > Object & Data, you can do it with several objects, or, for a single object, go into the Object Data panel and click on the make single user button to unlink the mesh: