Sub power up does affect bomb launchers, but only under certain conditions. This Squidboard thread says it better than I can:
Does Sub Power Up affect Bomb Launcher?
Yes, it does but only if you throw it at max range. If you hold R your
inkling will throw them at maximum range/speed which will be affected
by Sub-Power Up while the R button-mashing that most people use will
not be affected by Sub Power Up.
It will probably be more effective to use special power up because then you don't have to worry about holding R. You'll be able to get more bombs out, ink more turf, and it's easier to trap someone with your bombs if you're mashing R.