Both slots are x16 slots, but the second only has x4 active lanes, making it 16 slot in size with 4 active lanes. But to answer your question, after reading a few articles around the web, yes there is a performance hit with using 16x4, but no it's not serious. Because the board uses PCIe 2.0, each lane has more bandwidth. It's only the higher end cards that need the extra bandwidth, if you are sticking to mainstream, then the performance gap versus an 8x8 or 16x16 will be about 5-10%.
The article here shows what happens when you run cards at various lane limits. At x4 speed, the difference is 4-5% drop in performance Vs. a x16 slot with a 5870. So in terms of crossfire, 16x4 will have minimal impact. The problem may remain with the drivers and if they can handle async PCIe lanes...
