FTL Firing weapons during stealth warmup period
I just tested this with the Stealth cruiser. On the first node I jumped to, I tested the following five times each:
Pausing, activating cloak, resuming, waiting 1 second, and then firing Dual Lasers
Pausing, activating cloak and firing Dual Lasers at the same time, resuming
Pausing, activating cloak, resuming and pausing before the cloak visualization has taken full effect, firing Dual Lasers, resuming
In all cases, the total cloak time visibly dropped by a bar once the weapon was fired.
I concluded that the game engine considers you to be cloaked from the moment the system is activated, and therefore that your weapons will affect the total cloak time whenever you activate them in that period (unless, of course, you have the Stealth Weapons upgrade.)
It is also worth noting that if you fire your weapons just before activating your cloak, you don't lose any time (even if the weapon is a burst weapon and is technically firing during the cloak charge, as long as the initial shot was launched prior to the cloak.)