Does adding a sub to a naval surface flotilla add to its invisibility?

No, but the subs can become unseeable in the fleet. IE, you have 2 cruisers and 1 destroyer in a fleet. You add 2 subs to the fleet. An enemy fleet may only see the 2 Cruisers and destroyer (depending on Scout exchange rate). But when it attacks, the subs become visible and part of the fight.