Here is a clear out about the way missiles work. Use this guide in order to time them with other attacks.

Points to take in mind:
-Missiles are not included in Split Second Feature
-Missiles launch is controlled by your account activity [Not the game engine like all other missions. For example, if you launch an attack against someone and then close your game window right away, the attack wil proceed normally at the exact time etc. Missiles will NOT. Missiles hit is checked every time you load a page (any page).]
-Missiles do not generate reports for attacker
-You can check if your Missiles arrived from your Overview screen. If they have arrived, you will see nothing. If they have not, you will see time remaining.
-Missiles are very fast, waiting time for them to arrive is minimal (still mandatory).

The reasons that missiles are not handled by the game engine but instead of your account activity are:
-Less load for game engine which already handles a lot of issues per second.
-Low necessity and usage
-In different situation, it would be more difficult to defend against missiles at all

Fixed the link.