For example, if you just hack the item Enigma Stone to get the Latios/Latias in HG/SS, will the Pokemon also be hacked? I want to be able to send some event Pokemon through Pokebank but not* if they're hacked.
No, it will not.
How you get the Pokemon is completely irrelevant; as long as it's history (i.e. location it was found) is legal it's perfectly fine.
Hope I helped. :)