Look up the way corn snakes are selectively bred in the USA sometime. By human standards it's worse than the Habsburgs or the Pharaohs, but it doesn't mess them up as much as it does us – it just brings out the unusual colouring (or whatever) that you want to produce.

If dragons were real, I dare say they'd be more similar in that respect to snakes than to humans.

But you're right that the ecological implications of having dragons are usually ignored. It would be satisfying to read something properly thought through about what a world with dragons in it would be like.

In Naomi Novik's Empire of Ivory (the fourth in the Temeraire series), there's a society in Africa where humans and dragons co-operate. Together they farm elephants (which obviously people couldn't do alone), with the result that there's a breed of domesticated African elephant which is docile and larger than wild ones. It's an interesting start on the question of how the existence of dragons would affect other species...