I'd say it makes a massive difference. In my opinion the intercooler doesn't need fans as the points in time where you want to cool the charge air is when you're on boost - motiring along at good speed with good airflow on the front of the cooler.

The important times you'll want to cool your water is when you're sat in traffic with no air flow at all and if your fans are pointlessly blowing air through the cooler when its not needed all your rad is going to get is any moving air that comes out the other side, which won't be much.

I'm sure other people will disagree but for me the fans need to be on the rad or you'll forever be wathing the coolant temps and having issues especially suck in queues in the summer, i.e. on the way into every show, ever.