I figured Atom had hyperthreading because it was Intel's first in-order x86 core in over a decade, so compilers had forgotten how to schedule x86 code, so there were lots of stalls in the ALUs that a second thread could make good use of. Plus scheduling for Atom is pretty hard in part due to the lack of registers in x86.

Additionally, Ars argues [1] that from a performance per watt perspective, hyperthreading makes more sense with x86 and two cores makes more sense with ARM

[1] http://arstechnica.com/gadgets/2008/05/risc-vs-cisc-mobile-e...