Hey Jay,
I'm far from an SF Bay expert, but I've been out there a dozen times or so in my old 19 Angler, and my current 22. On one occasion in my 19, and a couple in my 22, it turned ugly on me in a hurry - which I'm guessing you are familiar with, if you sail out there.
I didn't feel in danger with the 19 or 22, but it was no walk in the park...not sure I would want to experience what I went through in a 16.
Short answer...I think a 16 is marginal for SF Bay, if that's a routine destination for you. You'll definitely need to pick your days. Would it get you back safely, if things got ugly? Sure...probably better than any oher 16 out there, but still...it can really get rockin' and rollin' out there in a hurry.
Up the Delta a little further, I think your navigable days would be far more frequent. Ditto for the rest of the destinations you mentioned - it's an ideal boat for inland CA waters, if you don't need the size and additional creature comforts in the 19/22.
If you are thinking new, you might check in with the dealer in Alameda - the Outboard Motor Shop. Ask for Bill - he's the head sales guy, but he's very laid back and won't give you the hard sell. They have a dock on the estuary, and might have a 16 available for demo rides - wouldn't hurt to ask.