So the tips/notes says to try and not include את when using the future tense. Is this different when it's used in a question? Or would this sentence just be placing extra emphasis on the word "you" ?
Dropping the pronoun in second person future tense could be understood in Modern Hebrew as imperative. That's why generally we still use the second person pronouns, unless it's unlikely that the verb is used as a command -
Be at the market = תהיי בשוק. (You can also use the proper imperative tense: היי בשוק, but it's not common)
You will be at the market = את תהיי בשוק
When will you be at the market? = ?מתי את תהיי בשוק?/מתי תהיי בשוק.
Soon you will be at the market = בקרוב את תהיי בשוק/בקרוב תהיי בשוק
Since it's hard to interpret the תהיי in the last two sentences as an order, you can use it without the pronoun.
Regarding this sentence, if you say it with the right intonation "?תהיי בשוק" might be alright, but it sounds better with את.