No phase ship fights a fair fight.
Frigates can bypass shields by simply being fast enough.
Harbinger can disable shields, though not much after that since weapon slot nerf.
Doom can use mines as multi-directional attack to bypass shields.
Not completely fair, but also not completely unfair. Frigates have to show up to do damage and become vulnerable. Harbringer creates an only temporary window of opportunity and any other ship can still attack it. Doom can just attack you from behind while being invulnerable, and there's nothing you can do to stop it, you have to wait until Doom makes its own mistake.
Phase frigates and Harbinger are generally not very threatening, despite their annoyance, when piloted by AI - they are too cowardly and run out of peak performance quickly. Player on the other hand is much nastier with them. Afflictor is the Reaper murder machine. It was the Reaper murder machine in 0.9a, but Reaper Harbinger was more convenient. With that gone, I am back to chaining Afflictors to do what Harbinger used to do - murder big ships and battlestations quickly. Now that Harbinger is stuck with AM Blasters (or Phase Lances), AM Blaster duty gets delegated to Harbinger, while Afflictor gets assigned to Reaper duty.
As for Doom and mines...
Against some opponents who are ill-equipped to deal with mines, mines alone would be sufficient. (Such targets also tend to be helpless against fighter swarm.) Against enemies that can snuff mines soon after they spawn, Doom needs more than mines alone and either needs to brawl up-close where it will get shot (no more than 700 shot range) or rely on help from other ships to pin the enemy. This is when armor skills really help on Doom, and I build one officer specifically for a Doom. Doom will take hits if forced to brawl or otherwise decloak within firing range of the enemy.
I am not opposed for mines taking a second or two to arm, but beyond that they are not that unfair. It may force the player to fight differently than normal. Instead of letting your AI ships do as they please, they may need to be controlled more than usual. Players who normally deathball (to mitigate some other problem) or hang back for mass fighter spam may not notice Doom and mines that much. Also, I wonder if zombie industrial specialists even care about unfair casualties if they are built to shrug them off and recover and abuse clunkers. (I have not tried a dedicated zombie character yet.)
I would find mines from Star Fortress more annoying than from Doom, since Star Fortress can spam more (at least high-tech can), and can back them up with much more firepower than Doom can put out. Only thing is there is almost no need to fight them (when the main reason to attack a planet is raiding for blueprints, which bypasses the station), although mine friendly fire from your Star Fortress can be a problem.
When it comes to mines, I am more annoyed with friendly-fire problems caused by the occasional careless placement of mines by allied AI.
P.S. When I bring my Doom to fight endgame battles, it is usually the first ship to run out of peak performance, even with Officer with Combat Endurance (and no Defensive Systems to accelerate peak performance drain), and the first I need to retreat, especially with phase ships' faster CR decay.