I think the general idea was that, if I'm understanding it correctly, Military Orbitals were supposed to be the choice of planets that had heavy "turret" defense, especially on the wormholes, making them that much more powerful and scary if the enemy got caught.
Logistic Orbitals were probably better suited for planets with a "standing army", or, for example planets with an Ion Cannon since they already instagib anyway, and it gives them plenty of time to kill everything.
However, the problem with this is that, especially at Mark 1, the "damage boost" from Military Orbitals is so insignificant, while the slow/speed boost from the Logistic Orbitals is so huge, that at Mark 1 there doesn't even seem to be a contest between the two. If, for example, the Military Orbital was like a Fortress in its own right (which in my opinion it should be), then it could be somewhat of a standalone defense, allowing you to free up shields for use in other places, and taking pressure of planets that were constantly being raided by small forces.
At this point, its role seems to only shine when upgraded, but the cost of upgrading it is so expensive (5,000 for MKII alone), that I fail to see how you are going to afford this and the knowledge for turrets/defenses necessary to even get the kind of use out of it you would need, at least if you want to have any kind of army to attack with. I could possibly see some use for it in games with more players, if one person were to take the "defense building" role, and simply built MKIII Military Orbitals on "chokepoint" planets with a ton of upgraded defenses to make an nearly impenetrable gauntlet; but that same guy could spend all that knowledge on just upgrading mobile forces and building MK1 Logistics instead, and defend almost as well with a force that could also attack...
Suggestions:
1. Make them powerful "stand-alone" defenses (not as powerful as a Fortress, but definitely strong enough to withstand small attacks) but remove any resource bonuses it gives, making them purely "self-sufficient" after being built (maybe a small energy cost, but I don't think that would be necessary).
2. Make them give more of an attack bonus at level 1 (Maybe 1.4x would be nice).
3. Make them do full damage even while under a shield.
4. Make them cost less knowledge to upgrade.
I personally like the first option the best because it gives them a very "defined" role, and fills something that I believe is missing in the game.