Facehuggers, what is it with you and the crazy theories about pheromones? There's clearly no strange cooperation or symbiosis between the cat and the alien. Why would anyone in their right mind think of that?? Just because two species communicate by pheromones doesn't mean they can understand each other. Totally different biological and chemical protocols. :D
But the cat-alien relationship actually teaches us something important about the nature of the alien. The alien briefly investigates Jonesy at the end of the film and just slams the cage out of the way, a scene meant to show us that the Alien is somehow designed to detect and destroy intelligent, superior beings and that he's not at all interested in other inferior life forms, that it's not just a destroyer of anything that moves and lives. It makes the alien appear more like a programmed biomechanical being, desgined to kill sentients rather than it being an intelligent extraterrestrial, who would've been curious and intrigued by an unknown life form, even if it were a lesser one. This scene also dismisses the alien from being identified as a mere hungry, mindless alien beast that kills and eats anything that moves and strengthens the theory that it's more like a programmed serial killer, a living weapon rather than a functional, natural individual of an alien predatory species.
When everyone saw that alien-Jonesy scene for the first time, I bet that up to that point, everyone thought of the alien as a ruthless killer and I'm pretty sure that everyone expected the alien to kill the cat too or the cat serving as a distraction for him while Ripley sneaks past the alien, or with Ripley buying some time by sacrificing Jonesy to the alien. I think everyone was quite surprised to see the alien brush the cage aside and return to stalking and hunting for bigger game.
The cat is also a nice maritime history reference with the entire concept of the ship's cat, but it serves as a cinematic device not only as a silent witness, but also serves as a scare and tension buildup source (still cinematic devices). Remember the scene where Ripley, Parker and Brett mistakenly track and almost capture Jonesy instead of the alien and also the scene where Jonesy jump-scares Ripley (and the audience) by making some noises behind the pilot seats and jumping across the seats. Mhrreeeooow! Jones! Goddamit!
Jonesy also serves as a plot device, when Brett separates from the others to go and find him ("Kitty crap!") and gets killed. Also, remember Ripley turning back to get Jonesy, despite the ongoing countdown, while the alien has enough time to get past her and camouflage himself through the pipes of the Narcissus.
