How about a countdown that lasts about 30 seconds to a minute after an npc is alerted and it prevents all attacks against that npc that way you get to actually see alerts and have a chance on things like Silthion queens rather then having the alert box popup and clicking on it only to be told "This enemy has already been disabled."

You and I both know Sparky, That this only happens in a select few legions.
In the top legions, they are competed for, That's how it should be, this will just make it that 10+ People are hitting it at the same time.

There is certainly a delay, and it does need to be sorted, because it affects any alert that results in a red pop-up appearing, including planets being under attack.

The only way i know of for the red boxes to appear right away, is that you actually have to be doing something that affects your energy/hull or shields(or activating artifacts), which means NPC'ing, PvP or attacking a planet, but you cannot be constantly doing those things just to be sure you see all alerts as soon as possible.

Alerts like that should be automatically appearing and not just appear when your actually doing something on screen. Whats the purpose of getting an alert that your planet is under attack, if its appearing 15 seconds after the attack has begun, which is enough time to take a planet and flux it.