There is a limit to how many lanes can be used at once. If a board drops to x8/x8 from x16 (not all do, many stay at x16/x16, but those are costlier) it is because of limited PCI lanes.
As a note, many benchmarks show the hit to performance isn't an issue unless you are using two cards, that each on their own, saturate a x16 slot. Those cards are rare (4870x2, GTX295, 5870) so in general x8/x8 performs well.