Yes, the crit does apply to Rune Arm shots, at least in my experience. I often hold off firing the Rune Arm until I get the Versatile Empowerment buff (it comes pretty often) - a fully charged tier 5 Rune Arm with a guaranteed crit can be fairly devastating. And as someone else said, there are quite a few useful Artificer spells for melee combat which benefit from this (Prismatic Strike is another good one).