You have lucky sheep. They eat and you are curious what it is they eat. But our sheep in the sentence above are not that lucky. They were the ones being eaten. We are more desperate than curious and want to know what in the world ate them???
The Czech sentence would be "Co sežraly naše ovce" if we were asking what our sheep ate. SEŽRALO is a neuter singular past tense.
Not a native but I had studied the rule about it in a grammar book:
The construction What + ausiliar verb +subject +verb ia used when the information that we miss is the object (or accusative) of the phrase. Ex : what do you eat for breakfast? What have you eaten? What did you eat yesterday? So here there is "what" followed by auxiliary verb to be or to have
But in this case what is the subject of the phrase and not the object. So in this case we do not use the auxiliary. Just think about "who are you?", "What is it?" "Who is eating?" "Who ate my chocolate?"
So you can find: What ate my sheep? Who ate my sheep? = The wolf / my neighbour ate my sheep
What did my sheep eat? = My sheep ate grass