Via-in-pad can ruin a manufacturer's whole day. Or, if properly done, can go completely unnoticed. There are a number of ways to properly put a via in a pad but the best is to have it filled and plated over at the board fab house.
If you do that, check with them on their planarity standards. If they don't hold tight, you can end up with a dip or a bump where the via is. Neither of those are as big a problem as an open via, but they can still lead to some difficulties.
Speaking of bumps, the old standby, HASL, generally leaves bumps on the pads too. And, across the span of a BGA, the bumps can vary in size and shape. That's not such a good thing either. If you're designing with a fine-pitch BGA, you might want to consider a flatter surface such as ENIG or Immersion Silver.