Yes, this is a "restaurant" kind of phrase that a server might use to take your order. (It may have other uses, but I know it only in this context for now.)
I understand that in terms of context - yes, this means 'What are you having? '.
However, it's actually not though in translation- it's 'what are you giving yourself?' which is of course nonsense in English.
However it's not uncommon for a bartender or server to ask 'what will it be?' in English.
If you don't want to allow this - I think it's a bit unfair to have the choices available to build this (what will it be) sentence. As the answer is never going to be a direct translation and always a familiar phrase.
'what will it be?' is quite colloquial and we have a direct translation for that ("Co to bude?") while we do not have any other closer or more direct translation for "What will you be having?".