I just recently had to repair a small leak in my intercooler and a dab of JB Weld worked nicely. Then, you can test the intercooler by buying a bicycle inner tube and cutting it so yo can clamp a piece over one opening in the intercooler, then clamp a piece with the air valve over the other opening and test with your air compressor at about 25lbs of pressure. Don't go higher or the tube will pop.
I really don't think a small leak could negatively affect anything though. Paul