Im interested in running 2 GPUs in an SLI array. I understand that motherboards having multiple PCIe slots will run differently depending on how many card occupy the PCIe slots. Correct me if Im wrong, a motherboard with 2x PCIe slots will run at 16x with one card, or 8x and 8x when theres two cards.
My question is, are there any motherboards that support two cards both running at 16x? i.e. 2 cards running at 16x/16x not 8x/8x or 16x/8x)
Yes, there are motherboards like that. You can check out Newegg and they have a selection in the motherboard area for how many X16 slots the motherboards have. The motherboards go up in price quickly when you get a lot of X16 slots.
There are indeed dual x16 slot motherboards, but they tend to be quite expensive. In particular, the x79 chipset supporting the flagship LGA 2011 processors (Sandy Bridge-E) have more than the usual number of PCIe lanes, and tend to support this configuration.
However, an x8 slot will not handicap your performance, especially if it's on a PCIe 3.0 board. PCIe 3.0 has double the bandwidth of 2.0, so an x8 slot for PCIe 3.0 is identical in potential performance to an x16 slot in PCIe 2.0.
Even then, an x8 slot for PCIe 2.0 is more than enough for the vast majority of cards, and even the most demanding cards only see about a 1%-3% performance decrease. In general it's not worth worrying about how many PCIe lanes of what generation your board has as long as it's at least equivalent to x8 of PCIe 2.0.