When running an i7 4770k on an Asus Z87 Pro (allowing 16 PCIe lanes), with two GTX 980s (thats two 8x PCIe lanes), will having an Asus Essence STX soundcard cause a bottleneck by pushing the lanes being required to 17?
No, all of your other slots run on a PCIe 2.0 interface running at 8x. Common configuration is an x16 slot capable of 8x. Three 1x slots. When any of the 1x slots are populated the 8x slot can only run at 4x.
You should not be affected, the i7 4770k have 16 PCIe 3.0 lanes, that are used by your video cards, and the slower PCIe 2.0 are controlled by the z87 chipset: