In my vanilla 1.4 game: it affects only retainers. I think something is wrong cause indeed the only musket-bearing troops are the ones we bring in battle ourselves (the kokujins with their retinues). Levies never carry guns which is kind of weird since rebels can. Moreover, the manufactories produce large amounts of them and even when my standing army gets destroyed, I never risk of running out of muskets...
I think it is bugged or something.