1) Keeping the snakes well hydrated is good, but you shouldn't have to soak them for that--keep cage humidity high, and provide fresh drinking water. Keep temperatures about 5 degrees above normal. (Some recommend to lower humidity--this is incorrect, as it leads to dehydration and thickens the mucous. It makes it appear that there is less mucous, but actually it's just lower in volume because it's thicker--thinner mucous is easier to expel).

2) There should not be any residual symptoms after a RI has been successfully treated.

3) Are you sure that this was EVER a bacterial problem, or issue related to the bedding? How did you determine there was cedar in the cypress bedding? Have you considered that this may be a viral infection, and the bacteria were just opportunistic and causing a secondary infection? Usually, one or two animals might get an RI, if some stressing event or cold happens--not half the collection. That makes it sound like something contagious, and the failure of the vet to identify a single culprit...well, maybe the bacteria are innocent.

4) To help thin the mucous, you can nebulize the snakes using plain water. Funny as it sounds, hang them upside down for a moment, then wipe up. Snakes have no diaphragm, so can't cough, and tend to sit with their head elevated when they have trouble breathing. By turning them head down, they will often expel some mucous, and then breathe easier afterward. There's a balance between adding stress and offering treatment. Don't handle or mess with them excessively--try to keep it to once or twice a day, at most, for handling, and once a day for something like nebulizing, unless the vet directs otherwise and gives meds to put in the nebulizing solution.
(You may be able to rent a nebulizer, if you don't have one).
You can cut a hole in a bin, and put the nebulizer tube through the hole, so the tub fills with the mist, to do a nebulizer treatment.