The FMS in the -400 certainly does take temp. deviation into account, if you want to see it happen, next time plug in a + instead of a - in front of the temperature, associated with the winds, at altitude!
The FMS also takes into account the buffet limitations, before showing optimum and maximum FLs, that are pre programmed depending on what aviation authority they operate under, 1.3 for UK CAA and 1.2, (I think), for FAA.