The Alien: Ax's Cover Identity At School

[JackP]

I wouldn't find it unlikely for word to get to Tom about his cousin - maybe a non-Controller Sharing member might say something like "your cousin Phillip is such a weirdo!", if they had spent more than a minute with Ax :p

Though it could be hand-waved, maybe Tom might assume it's a cousin's of Rachel he and Jake don't share, or that Jake was lying about it for another reason.

I've worked in schools, and I find it hard to swallow that any stranger would easily be allowed in a school he doesn't attend.

[TheWolfEmperor]

Probably because Visser Three decapitates anybody who disagrees with him.  I suspect a great many Yeerks probably suspected the Animorphs of being human (the possibility is mentioned clear back in #4), but never said anything, for fear of suggesting that their Supreme Leader was actually being stymied by a bunch of human teenagers. 

This was mentioned in The Predator.

No, it was in #4 The Message. The Animorphs are investigating the beach and they run into controllers. After nearly being shot, they run into the ocean and morph into trouts, which was the only water morph they had at the time.

While they were swimming in the ocean water and feeling the burn of the salt-water against their freshwater bodies, they overhear one of the Controllers discovering and raising the question of the floating pairs of pants and shirts. That's when one controller, possibly Tom, bring sup the possibility of humans and not Andalites being the real bandits. Chapman replies with, "Maybe, but I'm not going to be the one to tell Visser 3."