I saw a couple of threads about this and really need to do something about the water that collects in mine. I don't drive it much, and living in Ohio, I get the dreaded acceleration stumble when it rains. I was thinking about drilling a small pinhole on the lowest part of the intercooler. I just can't picture if that would affect the boost pressure in any noticeable way, since the hole will be pretty small compared to the volume of air pumped by the engine.

Another option is to install a drain, which is great except the installation would require a long afternoon if not all day...

 

Look in the tech folder, their is a post on installing various drains.