1) Deterence- With a magazine inserted, I maintain the illusion that the firearms IS loaded until police can confirm otherwise. Criminals don't know this and must assume that it is loaded and ready for use.
2) Legality- There is nothing illegal about having an empty magazine inserted in your firearm. That being said, there is bad case law that exists in California that would lead prosecutors to conclude that a concealed magazine being an essential component to a firearm constitutes a "concealed weapon'- by having a 'completed' weapon with an empty magazine in place, you further protect yourself from other legal perils if that arguement comes into play.
3) Logical conclusion- If having a magazine in the well of an unloaded firearm is a bad idea, then could one also conclude that if loaded open carry was generally lawful everywhere in California, that it would also be a bad idea to have a full magazine in a loaded weapon as well? The answer to me is clearly no... guns are meant to be carried and used loaded, and therefore an empyy magazine is irrelvant to how it is carried.