Nope, I caught an Inkay with Pokerus, but I still got the same base stat increases as my other Pokemon, and I have to say I was quite disappointed, super-training basically makes Pokerus useless in gen 6. Super training is quick, and can be done anytime without battling. I maximised my new Pokemon's stats in half an hour - tops.
What a shame, such wasted potential, but I suppose Pokerus is still useful if you can't get your head around super training, and just want to E.V. train traditionally.