When I was home in CA a couple of weeks ago, I had to get a new sticker for the truck that my youngest daughter is learning to drive. I went to the local Navy base (Port Hueneme), and they had some kind of Navy Instruction there that said all vehicles they were issuing stickers to had to be able to comply with all local emissions rules and testing.

So it would seem that regardless of where your home of record is, your vehicle will have to pass smog in order to get it registered on a Navy base in CA. AF might be different, since they don't even issue window decals anymore. I'm the in USAFR, and get decals at the local Navy bases in CA and VA. Not having a window decal is fine if the bases you'll be going on are AF only. But in the Hampton Roads area of VA, like in San Antonio, there are more than just AF bases around, so it's best to get a window decal to cover all the service bases.