I only know the basics, but I think it might just be because that sentence can only be put as a question anyway. I mean, you can say “ni hao” to say hello, but you need to add “ma” if it is a question so people know it is a question. So ma is used when you say something that can be put as either a question or a statement. In this case, “what do you want” is only used as a question, so you don’t need ‘ma’ to signify it is a question, because you can’t say “what do you want” without it being a question.

Ni hao Skylar! I don’t need give you answer now. Pooshybooshy is absolutely correct! Xie xie ni Pooshyboosy!

Yes, ‘ni yao shen me?’ is already a question, so you don’t need ‘ma’ any more.

Another example:

ta shi lao shi = he’s a teacher (this is a statement)

but let’s add ‘ma’

ta shi la shi ma? = is he a teacher? (now it’s a question!)

‘shen me’ means ‘what’. It already indicates it’s a question. You don’t need add ‘ma’.