Yes. Which is why I consider them beyond the limits of the game, and thus, against the rules.
And I doubt MLG means glitches such as cloning, that is impossible to enforce. They probably mean things like using missingno in battle (or something similar).
I'd personally like to see evidence, or at least an explanation, of how exactly someone can determine if it's hacked or not. Is there information in the code that is written by the game that only the designers have? Information that programs like Pokesav do not write and cannot access? At official tournaments do they carry around devices that can detect if your game was ever touched by an AR before?
It's incredibly simple to create pokemon that appear as all others do using Pokesav - who can determine it's authenticity and how?
Also, from the MLG rules:
"The use of any hacked Pokemon is strictly prohibited. The term "hacked" refers to any Pokemon acquired and/or enhanced through third party cheating devices, glitches in the game, or any so deemed illegal way. Should you suspect your opponent of using hacked Pokemon, please submit a ticket."