Gen 4 games aren't DSi Enhanced games which may be the code used to separate the 4th and 5th gen games, other than that, its simply because of Nintendo only porting one generation backwards. Its like the only thing they do. They don't seem to like to dwell in the past so they only allow one generation back connecting to the current gen console or something.
Gen 4 games can be read by the Radar App to get the legendary Pokemon on there. I doubt that's the reason. Like I said above, they probably used the DSi enhancement as the source to do the port over.
Hacked Pokemon won't be able to get through since it used an outside media device not endorsed by the companies (Neither Gamefreak not Nintendo endorse the Action Replay, both have issued multiple lawsuits against, and neither will reimburse a customer who has had their system or games destroyed by the action replay.)
As for items, you cannot transfer Items forward. At least you haven't been able to as far as I can remember. It and HMs have been a constant block for transfers. Poke Transfer doesn't allow items to be transferred, so that being the last one may be the most relevant.
So neither hacked Pokemon from 5th Gen titles nor cloned items from 5th Gen titles should be able to move forward due to the coding locks in the new transfer system.
So if anything is altered through outside devices, Pokegen, Action Replay, or what ever, the system will not allow them to be brought forward.