。
How many pens does she have?
Literal
She [topic-は] how-many-本 pen [object-を] is-having [question-か]?
Counters in Japanese aren't optional — to ask 'how many?' you typically pair the question word 何 with the appropriate counter for the object. 本 is the counter for long thin objects: pens, bottles, trees, bananas, fingers, rivers, and (by extension) films, plays, broadcasts. So 何本 = 'how many (long thin things).' Reading note: the pronunciation shifts with the counter (一本 'いっぽん,' 二本 'にほん,' 三本 'さんぼん') in a pattern the counter system extracts from the underlying phonology of native and Sino-Japanese numbers.