What is your student population? EMT, Paramedic, Nursing, Respiratory Care, Community CPR?
When I orient students to my lab, I always encourage them to use their BLS skills. I also tell them they are NOT to do mouth to mouth; just a bag valve mask. Quite frankly, there are (relatively inexpensive) task traininers that have been especially created with hygiene in mind are are easily cleaned after use. Our $50,000+ simulators have not been designed in that fashion.
We try to import to our faculty that the simulators are not just glorified task trainers; but a tool where students can put all of their knowledge and skills together and provide full patient care in a realistic environment. It is my hope that they would also have the tools of their trade readily available to them, such as a BVM, to provide safe patient care. The asumption is that the students have already been checked of their skills with equipment and technique on task traininers and are ready to put it all together, so to speak.
If your faculty are really intent on using the pocket masks in simulation, I suggest you have a task trainer in the room (that can be easily cleaned) and do it side by side with the simulator for a near-realistic simulation.
The potential for cross contamination and introduction of humidy and microbes into the lungs of the simulator makes me cringe, personally. The simulator exhales, realistically; if pathogens have been passed by one person to the simulator lungs; the full room could be potentially exposed (asuming airborn variety) with every simulator exhale. Of course, I am a germophobe by nature so I may be a bit biased in my opinion.