Mark I Siege Towers have 426666 cap DPS against everything (no damage multipliers). That combined with cap health of 32 million they're actually very good.
Problems are the very low rate of fire, the low range, the average speed combined with immunity to speed boosts, and the difficulty in replacement.
If you look at the stats in comparison to other units, they are average turrets that can go through wormholes, but require irreplacable resources to build.
They were better before the Starship buff, but now? I'd rather have a Spire, Bomber, or Plasma starship.
How to use the asteroids:
Mark V: Ion Blaster > Penetrator > Attritoner > Implosion Artillery > Siege Tower
Mark IV: Penetrator > Implosion Artillery > Ion Blaster > Attritoner > Siege Tower
Mark III: Penetrator > Implosion Artillery > Ion Blaster > Attritoner > Siege Tower
Mark II: Penetrator > Ion Blaster > Siege Tower > Attritoner > Implosion Artillery
Mark I: Penetrator > Siege Tower > Attritoner > Implosion Artillery > Ion Blaster
I think you both over-value Penetrators and Ion Blasters, and under-value Attritioners.
Attritioners do a little damage per second, which is usually insignificant except against swarmers, but the feedback effect matters everywhere. It basically multiplies the damage dealt by your units by a fixed percentage, ABOVE any Munitions boosts that may apply. That adds up fast. Of course, you need caps to get any significant effect - a single Mk I Attritioner is kin of a waste.
Penetrators are good for killing heavily defended stuff under glass (Especially AI Home Command Centers), but that's about it. They don't do enough damage to matter against Motherships or their ilk, and the 1-shot-per-30-minutes thing makes them worthless against fleetships. Very situational, and basically a ranged cloaking version of the Spirecraft Ram.
Ion Blasters are worthless at Mk I, as you point out, but Mk II isn't much better since when you need them, you'll be facing either Mk III or Mk V ships. Combine that with low range and the large numbre of Ion immune stuff out there, and you get a fragile, irreplacable ship that requires significant micro to use properly.
My build order is Attritioners first, then Implosion Artillery (to sit on my chokepoint and free up my fleet). Then, if I've got a bunch of extra asteroids, I start grabbing Siege Towers, Penetrators, etc.