"Will she come?"
来ます is an intransitive verb. There is nothing that "receives" the action of 'coming.'
See dictionary: http://jisho.org/search/%E6%9D%A5%E3%82%8B
Transitive vs. intransitive has nothing to do with subject anyway, that's about if they can take a direct object or not. You can both use or omit the subject depending on context with both types of verbs.
It's not transitive, in either language, and transitive versus intransitive has to do with taking an object, not a subject. You could not be more wrong, and since this is a learning platform and your comment is so misleading, I felt obliged to correct you.
As to dropping 彼女・かのじょ; you absolutely can, if the context makes it clear we are talking about "her" (some previously mentioned, or obviously implied, female person). Without the context though, and since "she" is specifically mentioned, you should translate it into the Japanese.
は marks the topic which is known/contextual/"old" information. What comes after it is stressed. When you see it you can think of it as "As for...", "On the topic of..."
In 彼女は来ますか, 彼女 "She" is known information by the listener, and it is the question "Will (she) come?" that you want the answer to.
"On the topic of her....will she come?"
が is the new information particle and stresses the word that comes before it
誰が来ますか - "Who" is unknown information and the thing you want an answer to so it is marked with が. The action of "come" isn't in question, but "who" is doing that action. Question words like "who" cannot be marked as a topic with は because topics are known information that provide context and a question word is inherently an unknown.
It also sounds a bit strange to emphasize a pronoun like "She" 彼女 with が as generally if you are using pronouns rather than a person's name it is assumed the listener should already know who "she" is. Just as you wouldn't start a paragraph in English only using vague pronouns without ever mentioning whose pronouns they belong to first. This would only really make sense if there was a group of people in view and you wanted to single one person out, like pointing at someone and going "As for people who will come; will SHE come?"
Azraelious, I believe the present and future verb forms are the same in Japanese, so it would depend on context. I am not sure how you would say this in present tense without knowing what the conversation was that included this question. Does she come every week? Is she coming? These 2 examples are present tense to me. Please correct me if I am wrong. Thank you.