Replicated ships dissapear after 300 or 360 seconds, not sure which.  Been like that as long as I can remember.  It's very useful to use to throw a balance in your favor though.  Enemy has lots of Light Frigats?  Use it on Long Range Frigates.  Use the ability on whatever counters your enemy's main damage dealing unit.  (If they have Long Range Frigs as the core, which is common, then flak is a good choice.  Flak is also a good choice if you rely on carriers of your own.

-Twilight Storm