Do they eat bad fruit habitually, or are they eating bad at the moment, or do they have the bad fruit almost in their mouth and you are deciding whether to to tell them or left them find out on their own?
Seems like there might be some chance the question would be "Are they eating bad fruit?".
"Do they eat bad fruit?" seems like a wording with a low probability of me ever hearing it said, compared to related questions "Did they eat bad fruit?",
It's an example, so not terribly real world. "Are they eating bad fruit?" is a perfectly good translation of the sentence, "Ĉu ili manĝas malbonajn fruktoj?" It could be offered as another alternative. This whole thread started on why it isn't "bad fruits."
You are right that "are they eating bad fruit?" is a more natural sentence. Something.
Unu: Ho, ili manĝas fruktojn! Du: Jes, kial? Unu: La fruktoj en la domo estas malbonaj! Du: Vere? Unu: Jes! Ĉu ili manĝas malbonajn fruktojn?
As I noted above, "fruit" in this sense is a mass noun; a singular noun referring to multiple items. Since it's not referenced to a counted quantity, but instead the abstract idea of fruit, it's construed in the singular.
There are some cases in which both forms are grammatically correct, depending on meaning. >How much fruit did you buy? >I bought seven apples.
>How many fruits did they have? >Just three: apples, bananas, and strawberries.