There are a few pro's and cons either way.
Reference design uses good quality components across all vendor models (all the cards are made by PC Partner) but run hot and loud. Tolerable in a single card setup with moderate-to-good chassis cooling.
Non-reference card fall into two categories; factory OC (DirectCuII, TFIII, Windforce etc) which tend to be more expensive, but have beefed up power regulation and dual-fans (fairly cool and quiet.)
The second category is non-reference with standard clock rates and a single fan. These frequently sell at a lower price point because the vendor has reduced the build quality from the original reference design -cheaper VRM's, lower number of phases, and a PCB of reduced number of layers make the card cheaper to produce. It also makes the card less likely to have any significant overclocking headroom (hence the vendor removing shader unlocking).
One other point to remember is that the 6950 uses the same 5Gb GDDR5 that the 5000 series cards utilise, while a true 6970 uses the uprated 6Gb GDDR5 memory chips - hence the number of 6950 unlocking "failures" being largely down to the flashed-6950 not being able to hold the 6970's "stock" 5500MHz memory speed.