1. At this time, it is too unclear. One would think yes, but I personally am waiting for a Secret ID code (no, you can't find it in your game, normally...that's why it's secret) so that way I can make my pokemon more legit. (search for one of my other posts). Secret IDs are Nintendo's way of cutting down hacked pokemon, and differentiating your pokemon from someone else's, if both you and the other person both have the same Trainer ID (which can be seen on your trainer card).
2.Not really, but it is the fastest way, in my opinion to get hacked pokemon onto your game. There is another method that uses the GTS or maybe even the Hyper GTS to get them that way, but that is one method I never really wanted to research.