Hacked Pokemon don't tend to have glitches, unless its really bad, or if you were the one that hacked it into the game. And if you were to trade a Pokemon with illegal stats (such as 999 in every stat) it will reset when traded to another game* (I can only confirm this in Generation III, l have no seen this in other generations), probably because the hacked data is not transferred along with the Pokemon itself, and stays in the previous game.
Hacked Pokemon are simply Pokemon created illegally and entered into the game.
Bad Egg's only appear under certain situations when you are the one hacking in the game; those hacks will produce Bad Eggs as a way to police and prevent hacking. (They will freeze the game.)
So basically, receiving hacked Pokemon pretty much won't do anything because they are only created illegally, they are still "legitimate" Pokemon according to the game when reading it.
Nothing will be wrong at all as long as the game can read the data normally such as if you were to trade a hacked a Charizard into the game because you needed it for the Pokedex; it's still seen as a regular Pokemon.
(Although there may be different results with Pokemon like shiny Reshiram/Zekrom/Victini that simply weren't meant to be.)
Also I do not recommend getting into the mess that is hacks anyways, you never know what may happen since hacked Pokemon are never meant to be, and it is extremely recommended that you don't hack yourself, since there are side effects that affect your game itself.