San Diego, for example, stomps all over Austin in terms of software jobs, and Austin's hardware scene is laughable.
Big ones: BAE, Northrop Grumman, and General Dynamics. (Previously I would have listed Qualcomm ...)
A zillion biotech startups: I drive past at least a dozen near here every day: https://www.google.com/maps/@32.9104712,-117.2304182,18.57z
Rockstar San Diego seems to be hiring as far as I can tell.
In addition, a lot of manufacturing companies up in the San Marcos/Vista area all need automation programmers.
If you're not finding SD companies with software jobs, I'm very surprised.