it seems to be accepted, but frankly should not be (unless it's also a way to ask what the skirts are made out of?) What are my skirts, in english, could only be answered by, "they are cotton" or "they are rayon" or "they are leather" or maybe, "they are clothing, what did you think they were?" It's never, ever a way to ask which ones belong to whom.
Most common phrasing in English would be 'which ones are my skirts?'
I think in everyday English language, people are more likely to say 'which of these are my skirts' but when I think about it, 'which are my skirts?' isn't actually wrong. I think one of the reasons why it sounds a little weird is because if you don't want to say 'of these' you also probably wouldn't bother to specify skirts in the question - you'd just say 'which are mine?'.