。
What does she have?
Literal
She [topic-は] what [object-を] is-having [question-か]?
持っている is the standard ownership/possession expression — bare 持つ would be the punctual act of taking hold; ~ている turns it into the steady state of having. So 何を持っていますか? = 'what does she have?' (or 'what's she holding?' depending on context). Either reading is grammatically the same; only context tells you whether you're asking about her possessions or what's currently in her hand.