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Another fun one is the pipes in the Blackwood Company HQ, which you actually need to pick up to finish the questline.

Found out the solution! Turns out it was the reference bug at all. Items started to disappear, just like the symptons describe. So I've Installed the official Bethesda Patch, after reinstalling the game. Now the merchants behave normally, just following you if you get out of their sight. The Items don't disappear anymore.
Something else I've noticed is that the amount of creatures inside Oblivon Gates was getting progressively smaller. Sometimes I could walk entire parts of the planes or caves without finding single creatures. After I reinstalled the game and installed the patch, they started to appear in bigger amounts (just like it was before the problems started).
But now about the number of stolen items, It did not got back to smaller and more true numbers, but I didn't noticed any other unbelievable and non condicent increase either...
Thanks to all that gave me any help, problem is solved, and solution (at least for my problem) is found!