I have had things stolen out of my tent...but the culprit was just a squirrel.
As far as leaving a pack unattended, my thoughts are that the greater the amount of effort and the smaller the number of people involved in getting to where you might be influences how safe your pack will be.
On Whitney, leaving your pack at Trail Crest seems a pretty safe bet. Most people up there have had to get a permit, they've had to get in condition over a period of months, and they are accordingly more likely to have a sense of camaraderie with other hikers. Even if there were a bad egg, it's not so tempting to steal something if you are hours from the nearest road and can't easily escape with the stolen goods.
On San Jacinto, like the proposed site at Wellman, there are many people coming and going. Most of them have taken the tram up, and while some may be confirmed hikers and adventurers, there seems to me to be a greater chance of a dishonest opportunist happening upon your unattended pack, and the results would be disheartening.
So, I would probably hide it before or after reaching the divide, if for no other reason than knowing that I wouldn't be worrying about it on my way up and back from the peak. Easily done, no worries. On Whitney, there's nowhere to hide it anyway, but I would leave it without a second thought.
z