A Pokemon is considered hack if it has illegal moveset and ability (Magikarp with Hyper Beam or the Wondertomb.) and 255 EV in all stats. The reason is it hacked because the PID doesn't match whatever you have (like say...Shiny...Modest...all IV 31...all 255 EV). There is a program that can generate possible IVs, nature, ability, and shiny status. I used it myself.
Program in question:
http://projectpokemon.org/editing/pidivgenerator.php
Well, I would still say it is legit, but you have to throw your Pokemon into the Legality Checker to see if it is legit (most likely not). If you have a way to dump your savedata (assuming you are using a physical copy), you can use Pokesav to save your Pokemon as a .pkm file and use the Legality Checker to check.
Legality checker:
http://projectpokemon.org/editing/legalitychecker.php
As for EV Modifier: no clue. You could use Pokesav to give the EVs. =/ Also, if you can modify Pokemon encounter, you can just fight those that give 3 EV to whatever stat, like Machamp for 3 Attack EV.
I sorta found a way to get Pokemon from your retail game to your computer. It is done by a program called HyperGTS.
Edit:
Just use HyperGTS. It is better than Python method:
https://sites.google.com/site/pokencg/gtsemu