It should not have much of an impact on an inline fan's cfm. Keep this in mind though if you are only working with 36" in width: your cool tube will likely be around 20" in length and 6" diameter, so if you go with 4" ducting you will have to add two reducers onto each end of the cool tube which is going to add somewhere around an additional 8" to the length of the cool tube and you'll still need to account for another 8" from the two 4" ducts. So that might not fit without angling the cool tube from corner to corner. If you stick with 6" ducting from inline fan to cool tube and then out, you'll get better efficiency and it should just fit (20" + 12").Was gonna ask if these reduce the air cfm ,
http://www.ebay.com/itm/4-DUCT-MUFFLER-INLINE-FAN-SILENCER-NOISE-REDUCER-inch-four-in-carbon-filter-can-/221207066673?pt=US_Hydroponics&hash=item3380f7f831