As far campaign goes, Nids being outnumbered in certain sectors has much less to do with their fleet costs and much more to do with their "Threat Level". There are a couple of sectors they run rampant through though, and they're a bitch to get rid of once they're in. The troop damage they do means you cant just chain one invasion into the next. There's quite a bit of downtime regenerating troops so as to not risk getting hulked constantly. Especially as Necrons.
If the complaint is the player being outnumbered that's on the player.
To answer the OP, balance changes will affect the Campaign I'm sure. There's no reason to ever believe they wouldn't.
@alien109 if chaos lances get fixed, I think that the campaign will become harder. However I don't think that it will become impossible, because the AI doesn't kite very effectively in my experience. As the imperium, if you have some space marines with you, chaos is not much of a threat. As necrons it can be quite difficult if chaos ships are very far from you, since necrons are quite sluggish despite the teleports. I haven't tried tyranids yet, so I can't tell anything about them.