The issue is reddit doesn't store all the data in one indexed and centralized location. It was pointed out that "hot" and "top" sorting aren't just a sort, but literally TWO LISTS that are constantly being updated and adjusted. So if you remove a comment from one list or location, it still might exist in other places. Then when reddit software gets around to reconciling these differences, the copy that still exists gets pushed onto the other lists and returns.

I'm not trying to justify the system; it sucks and reddit is directly responsible for that. But it does seem like they're not intentionally restoring content, it's just a side effect of their bungled system.