It's long been shown that this WILL impact your hop utilization -especially if we're talking about the large stainless hop spiders that sit above the wort. -The stainless mesh acts like a heat sink and pulls heat out of the kettle, particularly inside the mesh where the hops are. The temperature inside of the stainless hop spider will be several degress below boiling which impacts the rate of conversion and you're ultimate hop utilization.
-I've found that when I use pellets if I just calculate IBUs for whole hops it's about right.
Adam