I have never seen any references to him having a beard while in the U.S. (except for a dubious quote attributed by a dubious CTist to the dubious Amanda Keller, in which it is claimed that Atta had a beard when she first met him). I have seen lots of references to Atta shaving his beard off in 2000 before he arrived in the U.S.

-- well spotted, that's what I wasn't explaining!

I didn't mention it before because I didn't want that to colour anyone's thinking, plus I'm still looking into her supposed claim, but it's no big deal, and as you've bought it up I may as well explain.
Quick version: most of the stories of Atta being decidedly non-Islamic (drinking, using drugs, going to clubs etc) come from Amanda Keller, who truther Daniel Hopsicker says was his girlfriend in the spring of 2001.
Keller recently denied this, and another man has said he was the Mohamed who lived with her. But Hopsicker says she's just been pressured to change her story, and claims it still stands up:
Events, however, continue to prove Keller's earlier testimony correct and right on the money. The most recent was the release over the weekend of the soundless suicide video of a bearded Mohamed Atta and Siad Al Jarrah at a camp in Afghanistan with Osama bin Laden.
“Mohamed Atta had a beard when I met him,” said Atta’s erstwhile girlfriend Amanda Keller over four years ago.
Despite the denial of Atta's father, who has previously proven to be an inveterate liar (and who was in Florida less than two weeks before the attack) that was Mohamed Atta in the suicide video.
And he was wearing a beard. Advantage Keller.
http://www.madcowprod.com/10042006.html
Hopsicker, then, assumes that because Atta had a beard in spring of 2000, he also had one a year later. And yet all the reports I've seen that mention this say he shaved his beard off before going to the US (the 9/11 Commission mention it also, here):
After leaving Afghanistan, the hijackers made clear efforts to avoid appear-ing radical. Once back in Hamburg, they distanced themselves from conspicuous extremists like Zammar, whom they knew attracted unwanted attention from the authorities.99 They also changed their appearance and behavior. Atta wore Western clothing, shaved his beard, and no longer attended extremist mosques. Jarrah also no longer wore a full beard and, according to Senguen, acted much more the way he had when she first met him. And when Shehhi, while still in the UAE in January 2000, held a belated wedding celebration (he actually had been married in 1999), a friend of his was surprised to see that he had shaved off his beard and was acting like his old self again.
We also know Atta had no beard for his famous driving licence pic, I think taken May 2nd 2001. And I've read a lot of reports of people saying they recognised him from that shot, but I don't remember a single one saying "but he had a beard when I knew him".
Anyway, this is why it matters: if Atta never wore a beard in the US (and as al Qaeda specifically said that was a bad idea, you're not supposed to look like the stereotypical Islamist, it seems unlikely) then Keller's talking about someone else. Proving he never did is problematic, but looking for anyone mentioning that is a good place to start...