I've tinkered quite a bit with shot size and snowshoe hares with muzzleloaders. They're roughly the size of jackrabbits, and though easy to anchor I try to balance pattern density and penetration in my shot choices.
At the lower vels of muzzleloaders, I settle on #5 for the minimum size to fully penetrate within range. That's to ease cleanup, because #6 will certainly anchor them, but leaves behind pellets in the meat. If it's mostly going to be close range shooting, I'll go to #4 along with smaller charges just to limit the # of hits. It's more a game of uniform patterns than dense patterns in my world, and a hit is a hit, so long as they can't fly through holes in a pattern.
Squirrels? All we've got are the little "red" squirrels about the size of a big hamster. I'd guess #7 1/2 for them, but someone else will have to pipe up for bigger squirrels.