For the Auxiliaries: Yeah, I just assumed it all happened off-screen. If the Animorphs were going through the trouble of briefing them on the War and telling them all the procedures of acquiring, morphing, and the dangers surrounding it (2 hours, etc), then I'm sure they would've gotten to the whole clothing situation in there.
Just remember that this was all happening in the last 5 books, so obviously they (The Animorphs/K.A.) had a lot more important, 'bigger picture' things to focus on. And with the series being a monthly title and all, not every detail could have possibly made it in there with the given time.
[spoiler=#49 Spoilers]As for the Loren thing... I think THAT is genuinely a mistake though. It's been a while since I've read the book, but I think she got the power and learned how to morph while they were running away from the Yeerks, so there wouldn't have been any time to tell her about clothing. It was most likely just overlooked by the author with all the crazy things that were going on in that book alone (I believe that was the book where the Animorphs were 'outed' by the Yeerks).[/spoiler]
