There is a possibility they have Myco or some other respiratory infection going on. I too am curious as to why you are hearing this only during the night. If you put your ear up to their chest what do you hear? If you hear congestion then you have an illness on your hands and they should be seen by a qualified vet. I suggest doing some searching online for rat vets in your area. Usually with lung congestion you can hear it all day long. Are you sure they are not chewing on the bars of the cage? I have two does here that do this. My main concern would be that your one has done this his whole life. Myco is something that doesn't go away. Either they have no symptons or they do, and most often it's something that gets worse. For does this can be a problem too if they are not spayed, as Myco can sometimes lead to Pyometra.
First I would suggest looking for a different vet. If you need help locating one in your area let me know and I can try to find something. Just let me know your location. In order to determine if your vet is qualified to care for rats I always ask a few questions first such as:
What bedding do they recommend?
How much experience has he/she had with rats? How long?
Are they willing to learn more from their clients about rats?
Do they know what SDA, Sendai and Myco are?
How many rat patients have they treated?
Another thing to consider is your bedding. What type of bedding do you use? Pine and Cedar of course are not considered a good choice due to toxic phenols in the wood which causes respiratory illness. Aspen, Carefresh Ultra, and Hemp are good bedding choices for rats.