Why not 'What did our sheep eat' or 'What were our sheep eating?' What ate our sheep is not correct.
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.