There's nothing wrong with via in pad per say. As other people have noted an open via in pad can lead to soldering issues as the solder is sucked down the via hole. Hand soldering you'll be fine of course, also for small runs the manufacturer can just pre-fill the hole with solder by hand with an iron or a hot air pen. This usually eliminates most of the aforementioned issues.
Doing it with a BGA can be funny, or sad depending on if it's your board or someone elses. The vias like to wick all the solder from the balls right to the back of the board, or at the very least make just one critical ball have a bad or weak contact. That's nice when that fails in the field 3 months later :)
For real production again, nothing wrong with via in pad, it's really useful in many cases. All you have to do is have your pcb shop fill the holes. I usually let them fill with non-conductive material and then plate flat so we end up with a solid metal flat pad to solder to. There's a little cost adder for this but really it's not that bad.
Just another trade off you have to make to see if you can afford the extra cost.