I feel your pain. I always feel it's a sort of harassment attack.
As far as I know, there's no way to disable the alerts. It is INTENDED to warn you when someone hostile comes into your system so you have a chance to respond to the attacks, but in practice, because those stupid default scout ships have weapons (no clue why, they are useless) it simply means you get hundreds of alerts.
Frankly, some of the default ships I don't get... the heavy carrier is okay, but the dreadnaught is too weak to even take on the weakest group of remnants, the scout has an utterly useless weapon that jacks up the price and slows it down for no reason, and the defense station is only useful if you immediately increase it's size by 50%. It's almost like they were designed for a different sort of game.