"Are there clocks?"
When you are just asking about the existence of something, asking in the positive or negative has about the same nuance as in English. "Are there clocks?" vs. "Aren't there (any) clocks?" However, when making an offer to someone, offering in the negative is slightly more polite and sounds more like an offer. ケーキたべますか？Will you eat (some) cake? vs. けーきたべませんか？Won't you eat (some) cake?
If your question is about が vs は, I think both are ok.
If your question is about あるか, it's probably wrong.
ありますか is of course correct, but I doubt あるか is.
It should be ある? instead. Or あるの？
According to https://jref.com/articles/interrogative-forms.118/ the か is hardly ever used with the neutral form.
Another source : http://www.guidetojapanese.org/learn/grammar/question#The_question_marker_in_casual_speech