So that is "do spiders eat cats?" And if so, the position of the 2 nouns in this sentence is rather irrelevant and comprehension is dependent on the knowledge that Žerou needs an acc. pl. to be found in pavouky and it if were nom pl, we would see pavouci? Have I got that right?
Let's say somebody is asking about eating habits of cats in general, this person can say 'are cats eating...?'. I agree that 'Do cats eat...?' is more common, but 'are cats eating...' is also used (e.g. Are cats eating your plants? https://planttimes.com/cats-eating-plants-maybe-cat-grass-can-help/). Would 'Are cats eating spiders?' be translated differently in Czech?