In my experience, Astro Trains require no effort to counter. Not even Counter Dark Matter. Just ignore them. They do nothing besides act as mobile tachyon emitters.
I don't think the problem with Astro Trains it that they are too weak, or anything like that. I think they're just uninteresting.
Imagine some more varieties of Astro Trains:
Resource Trains - Pop them like Distribution Nodes to get resources, or lose them.
Reserve Trains - Like Zenith Nodes, but of the AI's current unlock types. Sometimes they could be trapped, and the ships that appear are hostile.
Warp Trains - Like Warp Guardians, but on a fixed travel route.
Counter-attack Trains - When destroyed, they trigger a small Counter-Attack wave.
Calling Card Trains - Every time they enter a Wormhole, they spawn a small group of AI ships to leave behind.
High-Energy Core Trains - When destroyed, they explode in a high-power, large radius AOE that hits everything (human or AI).
Prototype Trains - Drop a foldout that allows the player to build a single building (Trader good, for example) in that system. Doesn't come for free, just allows the player to start 1 building of that type.
Translocator Train - Fire Translocation shots. For more fun, allow them to send ships to other systems. For even more fun, allow them to teleport turrets, too.
Teleport Train - Doesn't move normally, just teleports.
Teleport Damper Train - Prevents teleportation or translocation while in system.
"Clear the Roads" Train - Continually fires a high-power Photon Beam Cannon directly ahead of itself on the path it's travelling.
Beachhead Train - Causes the player to die when it travels through the home system.
Beacon Trains - While in Human Space, they trigger small Exowave-like spawns that rush to the Train's current location.
Planetary Effect Trains - Armor Boost, Radar Jamming, munitions boosting, etc, for whatever system they are in.
Forcefield Trains - Has a large forcefield on it, pushing other stuff out of the way and protecting AI units.
ARS Train - Replaces a normal ARS. When killed, it drops the ARS into whatever system, as if it had seeded there.
More varieties of Turret Trains - Different shot types, different multipliers, ranges.
Data Trains - Destroy for a small AIP reduction.
You could work them in with Hybrids - That Advanced Hybrid plot? It needs special parts to be transported to it - by Astro Train. Find and destroy the Train before it gets to the Advanced Hybrid to (temporarily) derail the plot.
All sorts of things to make them more fun to play with. But right now? As you said: Just ignore them.