The nuke, EMP, shield, and cargo trains are intended to be killable with concentrated effort. Any of the others will be killable with
seriously concentrated effort but we're basically talking the moving equivalent of killing a wormhole guard post
And if the train population drops below the cap it'll eventually spawn more.
The idea isn't really for the player to be able to stop trains overall, otherwise it's just X more things to kill every Y minutes and we've got plenty of ways you can get that already.
The idea is for the player to be able to bend-but-not-break when the wandering-debuffs (i.e. trains) are in the wrong place at the wrong time (from your perspective). The trains themselves won't kill a thing, other than the nuke train (which seriously is only on the highest intensities, and you might see one or two per game if testing is any indication, and yes shooting it down prevents the nuke). It's all in the emergent interactions with other threats, which I think is one of the stronger points of the game.
Bear in mind that these are generally dangerous if they're on a planet you're attacking, not just on planets you're defending.
Will astro trains be the most popular option now? Rather not, I expect, but they'll be interesting (the current ones are really not), and in a way that nothing else currently is