The singular form “eats” translates into Russian as «ест» and direct objects of verbs are put in the accusative case, which coincides with the genitive case when the objects are humans or animals. Therefore, the Russian for “What eats horses?” is «Что ест лошадей?». The presence of cases in a language makes it flexible in terms of the word order; in other words, most of the time, the word order doesn’t matter. Intonation does though. You can say, «Что едят лошади?» or «Что лошади едят?» - both sentence are common and have the same range of meanings. By stressing «едят» you will be saying, “Now that we’ve discussed other aspects of [the] horses’ life tell me what they eat”. By stressing «лошади» you will be saying, “Now that we’ve discussed other animals tell me what horses eat”. By stressing «что» you make the question sound like “What is that that [the] horses eat?”
Yes. The что-subject-verb questions are mostly used when you make inquiries about definite subjects. It should be noted though that definite subjects are never stressed. For example, Что СОБАКИ едят? means “And what about dogs - what do THEY eat?” whereas Что собаки ЕДЯТ? simply means “What do the dogs eat?” or “What are the dogs eating?, depending on the context.