Phase ships are underpowered for AI. They often overextend, flux out, and die without doing anything. Doom is ok in AI hands because overpowered system and too slow to outrun your fleet. Half the time though, enemy ai deploys it late, so it has no support. It gets surrounded and dies. Shade and afflictor are also ok because they are basically a fast frigate that can go invincible and gtfo whenever they want plus antimatter blaster exists. But they are so fast, they often die on first contact or the enemy AI is too skittish to bring them out of the battle line where they can shine. We don't talk about gremlin.
Harbinger is, like most destroyers, too slow to get in, kill something, and get out; doesn't have the potential system range of doom to support the fleet; and the opening the system creates is so tiny the ai has trouble abusing it, not to mention the damage debuff from the system. If it overloaded for maybe a second longer so the AI has time to realize the enemy is overloaded and they should shoot it, it'd probably be ok. OR if it had more range and the AI could coordinate or realize an enemy has a bunch of damage aimed at it. There's also the problem of where to assign the harbinger, again like most destroyers. If the harbinger is safe in a battle line, it is too far to use its system and weapons without being in serious threat. So then what about hunting stragglers? I would prefer an afflictor or shade. Both much faster than the harbinger so they can catch even the fastest enemy running around and 2 afflictors > 1 harbinger. And both those ships work better in the battle line either swatting fighters or debuffing enemy.
If you can't tell, I just really dislike direct combat destroyers. When you need either range or speed to be effective in combat, the destroyer, which has neither, just sucks.