It's common enough, but it depends on the person. Some people never say it, others say it quite often, some only say it in a sarcastic way, etc.

As stated by the first answer, depends on who is speaking. It is common, however. To some people it feels more polite to use adverbs other than "what". For example; if someone calls someone else, and that person may say, "What do you want?" This can be better said as "How may I help you?" It is less abrasive.

Thank you :)

I would say, "In what way do you mean?"