Would the A16 properly emulate the sound of a subwoofer? And how would that work exactly?
Would it EQ a headphone like the HD800 (which does not have that much bass) to have the appropriate amount of bass that the subwoofer is outputting in a particular speaker setup?
Clearly the A16 cannot make headphones generate a frequency that is below (or above) the physical capacity of the headphone to produce. I think that your guess is right, in that the A16 will effectively eq the headphone so that it is able to produce a frequency range that reflects the actual system being modelled, but for a true audiophile frequency response you could always use a subwoofer in tandem with the A16: either output from your amp/player or ... am I right in remembering that the A16 actually has a subwoofer out??
In any case, when you take your readings I imagine that you have two options: to do them with the subwoofer connected or not. Much the best approach would seem to me to do the settings with the subwoofer off so that the A16 only ever models the sound in the audible range, without having do calculations for subsonic (and close-to-subsonic) bass. In that event the A16 would never even "hear" the subwoofer so the question wouldn't arise: but you'd have to remember to set your bass crossover so that the speakers were pushing as much of the audible spectrum as possible. (I have my crossover set quite high normally so that my sub shares some of the work with my small surround speakers.)