"What’s the protocol for notifying the owners of the cabin or cabins he breaks into? Of course, he’ll replace anything he took and have the windows fixed, but technically, he’s breaking and entering."

Where I live, the county prosecutor has considerable latitude when it comes to filing charges. I can't imagine a jury convicting Joe as long as he has made restitution.

"Does this change if someone stays behind in an area that’s being evacuated for flood, fire or hurricane? Where is the line between looting and taking for necessity?"

This could be an entirely different animal. In the case of large-scale disaster you could be under martial law, and subject to being shot on sight. I'm sure that being shot for looting is a rarity, but I wouldn't chance it. Obviously if there are police or Guardsmen in the area you'd have a way out. If I was going to stay behind I'd make darn sure I had what I needed and not go "borrowing" from my neighbors.

Regards, Vince