You have several decisions to make here, and none of them involves grammar, but style. You should thus be guided by your manual of style. I use the Chicago Manual of Style for the following topics.
First, you have to decide whether cui bono is sufficiently well understood by your audience to warrant dropping any emphasis to note it as a foreign phrase. CMS advises that "for doing this there are no guides but sensitivity and common sense." If the phrase is sufficiently foreign, italicize it and translate it.
If you opt for translation, CMS recommends that the translation appear in parentheses or quote marks. Dashes are reserved for asides, additional text that is loosely related to the rest of the sentence. This would not seem to cover a phrase and its translation, which are more tightly bound.
The decision to use quotes will be based upon whether you're actually asking a direct question, which itself must be in quotes.
Finally, you must decide how precious you want to be. Right now you've got a fairly familiar Latin phrase and two English phrases. You could balance that with your own Latin. Try this:
The question is not simply cui bono, "Who is it that benefits?" The
question is quid bonum, "What is that benefit?"
I've opted to place the Latin in italics and the translation in quotes. This means making the question an indirect one obviating the need for additional quote marks. I've also balanced the two parts of the paragraph, making both English parts and Latin parts parallel in diction.
But this is a stylistic choice, perhaps not one that you'd favor. You should make your choice based on what will make it easiest for your reader to follow your point.