I guess I'm just concerned about if his swallowing issues would be worse if his tonsils come out...
He will probably be admitted to a floor in the hospital where they specialize in breathing issues, or maybe even the ICU just for observation. I work on an airway floor and we share our floor with ICU (peds hospital). I often get the post op cleft palate repair kids or T&A kids who have swallowing issues. Most of the time everything is fine and they go home on schedule, but once in a great while we have to intubate to protect the airway. (Not to scare you- it's rare but it's good they are near help if they need it)! The biggest issue we have is T&A kids in the 2-4 year old age grou, or special needs kids of all ages, who are so sore they refuse to drink, eat, or take their oral medications. Oftentimes those kids are readmitted for a few more days and treated with IV meds and fluids until they feel well enough to start taking things by mouth again.
As far as whether or not swallowing issues would be better or worse after surgery-- I'm thinking a consult with a speech/feeding therapist might be a good idea.
Good luck with your decision!