I don't know why, but for some reason I keep thinking there's a penalty for using them (doing a stealth run), don't know why, so I just want to be sure that there's no issue/ penalty in using them at all.
Oh, neat, so it'd be like killing them with the main/ custom, huh? Good to hear, guess it makes sense since there are some areas that would be near, if not completely impossible to stealth through without Subs.
Actually, for completing R-07 with complete stealth, I killed the guard from the gate with a Homing Missile, and then distracted the other two with the Red Phosphorous Grenade, leading them to their death with executions. So yes, you can use them for stealth.
PlayStation Network: DarkEmigaru98 Youtube Channel: http://www.youtube.com/user/Emi3280