The purpose of an intercooler is to cool (making denser) the compressed air (heated by the act of compression). Since most roots type blowers mount directly to the intake manifold the intercooler would need to be sandwiched between the blower and the manifold, puts it pretty high up and makes the plumbing interesting depending on whether you cool with air or "water". There are other roots blowers that discharge through the front/back/or side and again, more plumbing issues.

It's not impossible, just not frequently done.