We recognize that animals have varying levels of intelligence. Why wouldn't an advanced, space faring civilization distinguish between us and maggots the way we distinguish between fish and dolphins?

It's more likely that they don't distinguish if they visit, because they're not here to study or make contact, but to extract resources or remove the solar system out of the way. Not too dissimilar to how clearing the amazon forest. There's no need to ask the native animals living in the forest for permission to clear it.