Could always just yank the fan plug and see what the noise and temp differences are.
The Sonata is not designed to be an "enthusiast's" case....Just the one case fan. Unless you have a big gaming GFX card or are doing more than moderate OC's, this should not be an issue, Does the GPU fan exhaust air outside the case (two slot design) or into the case (single slot design) ?
How did the slot cooler wind up in there ? Was it something you put in on a whim or was it recommended to you somehow.