Of course, a muted instrument will behave differently than an unmuted one in Real Life. Apart from the different Directivity Profiles (i.e. the way an instrument emanates certain freqencies into certain directions), MIR's Instrument Profiles also take into account the original recording setup (i.e. the position of the microphones in respect to the recorded instrument), as well as the tailor-made Character Presets and the Natural Volume Settings. You will lose all of these when you don't use the actual instrument's Profile.
The actual difference will depend a lot on the context, though. It might very well be that you won't notice too much difference in the way the instrument interacts with the room from a certain position in the stage. You _will_ note the difference when you use Character Presets, for example.
That said, you could have best of both worlds using Groups and the Icon's Hide-option. Just group all aspects of both the non-sordino as well as the sordino-strings, but one on the top of the other, and "Hide" one of them from the Venue Map. You will be able to control all the grouped aspects of both (or more) Instruments on behalf of one Icon. - Hidden instruments will remain visible in the Instrument List, of course.
HTH,
