I would think that is is not normal practice to run water piping through return air ducts. Most likely the plumber did the plumbing before the mechanical contractor did his work.
Not sure of what the codes are in your area but I don't think this will hurt the flow of air for your furnace or AC system. It will not harm your water piping other then if you have very warm weather and you flush the toiler a lot then the water flowing through the piping may be cold and the pipe may sweat causing some dripping. If you live in an cold climate area the water in the pipe will get much colder in the winter and may sweat. If you have not had any problems so far you may be ok. If there is a way to check the area in the return duct where the pipe is to see if any sweating has been taking place it would be good idea to check. If this area is in your basement and the piping is easily accessible then you may want to have a plumber relocated the pipe.