I flew out of SAN about 50 times last year, and with the exception of the 1, 1a, 2 Southwest gates, have always received full pre-check. I think OP had a weird one-off.
The use of canines by TSA is not new. Dog sniffs for explosives, WTMD looks for metallics. The big problem is the number of dogs required for full time screening. I don't think the pipeline would ever meet TSA's needs.