We don't have native "soft shell" crabs. I think they are mostly blue crabs from the east coast, or other asian species which are available here. If you are eating at a decent restaurant, you should expect that wherever the crabs are from, they should be good. Just like the steak you just ate didn't come out of the bay, neither will your soft-shelled crab dish. However, both may be tasty and fresh.

ps - how long have you lived in the Bay Area?