Since there's a balance manager who is the chief of all the various item counts I'd say that he/she is the person to decide.
Back in the days people used to copy items as that was possible due to a bug. I'm sure that the copying caused an imbalance which can be fixed by not putting such an item back in the loot pool.
As for the rest of the items I don't see a reason why they shouldn't be put back to the loot pool. It shouldn't make a difference if it's an uber item or not. Uber items are uber items due to their statistics and most of all due to their rareness. But I don't think that MA decides these things based on uber or not.