So in a normaly game when all of one sides ships are destroyed, all the squadrons count as destoryed.

Now based on points this would also applu to the CC campaign. However would tbose squadrons be counter as scarred. They were not destoryed, just the carriers were. On could argue the rebels ships could hyperspace back home, while only a few of the imperial ships could hit hyperspace.

And what about if all the ships jump to hyperspace, are the squadrons left behind to die in the cold heart of deep space?

This was discussed and answered int he "Hyperspace and squadrions" (more or less what it was called) thread.

No, they're not scarred, they merely count as destroyed for victory points purposes.

The same applies if every ship on one side warp out.