It's a KASU.
As you said, kafit are part of the starter pack when you start learning to morph, as per this extract of The Andalite Chronicles (this is Elfangor talking):
An an Andalite aristh, I'd been trained in morphing. Back at training they first transformed us with the morphing technology. And they gave us a djabala to acquire and morph.
A djabala is a small, six-legged animal, maybe a third the size of a young Andalite. It has a mouth and a tail and no natural weapons. It lives by climbing trees and eating the highest leaves.
You have to morph the djabala in order to pass the morphing proficiency test. So I did. But then, like a lot of arisths, I morphed a kafit bird. I have heard that some planets have many types of bird. But since we only have three, and since the kafit is the best species of the three, it's popular with young cadets looking for fun.
The Andalite Chronicles, chapter 13 (emphasis mine)
The "other native animal" you remembered is the djabala, which is mandatory. The kafit is popular, though. It's not unlikely, then, that Alloran would have a kafit morph, even if it's not obligatory. This is confirmed by the fact that this "Yeerks have infiltrated the home world" is never actually brought up again.
This headscratchers list (Warning! TVTropes link!) analyze makes a point:
It would be difficult, if not impossible, to infiltrate Andalite society at this point. The Yeerk invasion plans rely heavily on not being noticed. There's no way to get a Yeerk pool on the planet, and since the Andalites know about Yeerks, they could just starve any suspected Controllers of Kandrona rays very easily.
... And even has the courtesy to redirect us to this forum post with a Word of God:
1.) In book 8, Alloran (while tempoarily free of Visser Three's control) informed Ax that the Yeerks were on the Andalite Homeworld. This theme was echoed in book 18 (Ax gets worried when Visser Three morphs an Andalite bird), but it seems that nothing ever came of it after that. Is there any particular reason you dropped this plot point?
- Yes. We probably forgot it. Sometimes when you write a series you sort of scatter seeds, hoping one will grow. Unfortunately many are just eaten by birds.
Just to clarify: this seems to answer "Why was the Yeerks invading the homeland never brought up again?" rather than "Why was Ax surprised?", and it does, but Ax's surprise was precisely intended to bring that plot point (and The Andalite Chronicles came out later). Apart from that, it's worth noticing that he's shipwrecked on an alien planet (Earth), disconnected from a good bunch of things he knows, and has just been faced with
Supreme Leader evil chief Visser 3. He's likely to jump to conclusions, adrenaline kicking in and all.