Yeah, this doesn't mean they were hacked. "Egg apparently hatched" shows up when you have a Pokemon that wasn't bred/wasn't hatched on that specific game; ie, trading. Also, with the ability to trade long-distance, Pokerus is far less rare than it was in the other Generations.
Now if you were to check his Pokemon's stats, and we found they have a bunch of perfect IVs, then suspicion is raised, as we all know that being Shiny and having amazing IVs is, while not impossible, extremely rare. Another definitive check are the EVs, making sure how many they have is truly the max amount possible (if I recall, it's 510 total?).
That's a true hack check.