I suspect the question is intended to ask "What time do you eat?" I have never heard anyone ask the question "For how many hours do you eat?" and can't think of a situation when the question might be appropriate unless it is referring to a religious or cultural tradition of some kind
I believe the correct response to this is, "Unakula kwa masaa mangapi?" While "saa ngapi" can refer to asking what time it is, when the word "hour/hours" is used as a noun it is "saa" in the singular and "masaa" in the plural. "Mangapi" agrees with "masaa."