Warpgates, allow raids to enter your system directly from the wormholes. when it says 'x number of y ship are attacking z planet in *time*'
If you leave them all alive, then the AI will be able to send those into the depths of your systems, and youll have to put turrets or military units quite literally everywhere. This is rather bad, in my opinion.
Taking out warp gates, while increasing progress by 10, also means that you can actually set up a front, where no AI ships can get past. Concentrate as many turrets as you want into a small area, making a much more effective killzone.
Think of it territorially, its easier to defend a single border, but when you are surrounded and the enemy is coming from within.. well, not very good strategically.