The comedic implication is that the giant eagles are natural predators of goblins and, more importantly, hobbits. And might be inclined to a mid-flight snack.
Well they might easily see goblins yeah, that's probably why they hide from them.
But they're sentient and hobbits are the friends. Like I've never thought about eating a dog despite me eating pig all the time, and the difference isn't much more than between a goblin and a hobbit.
Yes, if taking it seriously, then those are reasonable conclusions. However, I think you're just overthinking it, in this context the scenario exists to service the joke rather than the other way around.