When I was watching SpongeBob, You're Fired! I thought about this when this happened:
It's not as weird to me in episodes like Dying for Pie, because it's more like Squidward hates SpongeBob, but deep down he cares about him. But in the quote above, it's kind of strange how they both acknowledge it when in most other episodes SpongeBob seems to be completely oblivious to Squidward's hate.
Or more likely, SpongeBob just doesn't care what Squidward thinks, so he just does whatever he wants. Squidward thinks he's annoying, but cares about him.