yes, since the there are only 2 physical cards, if the motherboard supports 2 x16 slots, then it doesn't matter that the card has 2 GPUs, you are still only running two cards.
Ohhh so youre using 4870X2's ? If so then hell youre fine with basically any crossfire capable motherboard. If you get a 790FX chipset or X48/X58 then youll be running at full 16/16. No need to fear. It may be 4 GPU's but its still only two cards.
Sorry, I missed the part in your OP about you using two X2 cards.