More PCIe lanes allows more bandwidth. So the fewer lanes each GPU has, the lower the bandwidth between your GPU and the rest of your system. While that sounds bad, in real world situations the even high end GPUs don't need all the bandwidth of a 16 lane PCIe 3 slot.
Assuming you're talking about PCIe 3.0 slots, two slots running with x8 lanes each is generally plenty even for an ultra high end setup. If it has to drop to x4, (or you're looking at PCIe 2.0 x8 slot), then with high end gear you might start to see some bandwidth constraints that could affect frame rates. Also, Nvidia SLI requires x8 slots, so you can't enable SLI for any card in a x4 slot.
If your mobo runs two x8 slots, then it's fine for dual GPU. 3xGPUs wouldn't go well in your motherboard, but it's very rarely a good idea anyway.