No difference in performance, they will still be matched pairs, but obviously 2 x 8 is preferable for future upgrades, with 4 x 4, all your RAM DIMMS will be taken up and you'd have to replace some or all of the RAM you have, 2 x 8 leaves 2 spare so you can just add 2 more DIMMS.
2 x 8gb may also be (if only notionally) less stress on the memory controller, and at the current PCS prices seems to generally be cheaper. So there's not much reason to get anything other than 2x8gb.
If you're going for a system that supports quad channel memory, then you would prefer 4x4gb.