the atom can reach 90C, sure. It sure as hell doesn't want to be run at 90C for any length of time though. The gpu will also underclock and throttle down in the 70C range.
What i see on my mini 9 is a drastic drop in performance caused by auto-throttling once i hit 70C. This does not halt the rise in temp though if i keep doing whatever it is i'm doing, which makes me think that it's mostly gpu throttling that's occuring, as the atom's throttling occurs at a much higher temp.
The mini9 would definitely benefit from having some air movement inside the unit, the only thing i would be concerned with is if the fan can get the air to where it's needed, without being too noisy to be useful.
just so you know, there is a EM shield behind the vent on the side of the mini-9, it's easily removable once you open the unit though. This EM shield greatly blocks air flow, as you'll see when you open the mini up and look at the vent from the other side.