It doesn't make a difference, but it makes it easier to suggest possible options for you.
I don't know why anybody would want to remove a fully functioning a/c system, especially in California, but to each their own I guess. It all depends on your plans for the car.
What do you mean by "clean up the engine bay"? If you're leaving your engine stock, it's not worth the time. Who wants to show off a stock Y code 307? A/C systems aren't the source of the underhood clutter, it's the complex emmisions system that you'll need to leave intact since you're in CA. Not worth the effort if you ask me. But what do I know...
If you wanted to retain your heater and defroster for the sake of being able to drive in the rain without your windows fogging up or to have a little warmth since it does get cool in cali every once in a while, you could go with a factory style non a/c set up. That way you still have the benefit of warm air, and they also feature fresh air vents similar to that of the cars of yesteryear...
But if you want to get rid of it all, remove all the components like the compressor and brackets, and just unbolt the box from the firewall, pull it out, and get a blank plate to cover the hole. People sell pre-fabbed block-off plates, or you can make your own with a little time by tracing the gasket from the box onto a piece of sheet metal. I personally think that the plates look out of place on anything other than a pure race car.
Also, freon is hazardous to the environment, and you'll need to have it removed by a local shop. Any garage in your area will be able to evacuate your a/c system, and I bet they won't even charge you for it.
I'd leave it as is, but it's your car...