I recently lost a rat to a respiratory infection that just didn't get better. The owner turned him over to me, he was sneezing, weezing, and hacking. His eyes were watering and his nose was running.
My vet treated him, but he was too far gone. Its definitely not something you want to let go on the off chance that it may just get better by itself. I can be caused by any number of problems... but mainly I would attribute it to substrate problems... and maybe a drafty cage. Need to address everything so it doesn't come back again after treatment.
Hope she does better.
Rav