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For low n' slow, bone-ins are better. Since they are whole, they have less surface exposure to bacteria. With a boneless, you're taking some of that exterior surface, and rolling it back into the center of the hunk of meat, where it will sit for several hours at low temps that bugs love.
I've used boneless butts for a few different things (jerk pork is a favorite), but not low'n'slows.