Well, astro trains are a ship category that is enabled by default, the Neinzul Rocketry Corps are a niche minor faction that is disabled by default, and can afford to not fit with every game
But, for perspective, please realize that these things only generate a warhead about every 15 minutes, and in the next version there's only a 1/15 chance of it being an emp warhead which works out to about once every 4 hours on the average.
Further, there should generally only be something like 6-7 of these in the entire galaxy on an 80 planet map.
Probably what I would do is just not capture the planet, or at least not put a lot of importance on keeping it, and just station some stuff around it to take out the warheads as they spawn.