The easiest way to evaluate effect of FPSWA's is to run your application in both modes, assuming that you don't care about separating the effect of SIR stalls from FPSWA events. However, it is quite possible for the (much more frequent) SIR stalls to take more time than FPSWA. Both events are eliminating by setting ftz. You can change the flush_to_zero mode by executing the intrinsic in
ifort -O3 implies -ftz, so you may want to set -ftz/-ftz- yourself, to over-ride what is implied by the optimization level.
Time spend in FPSWA's is likely to be included in the difference between your user and system time. So, if that difference is negligible, you needn't be concerned about FPSWA's.