Vagrant: It's not supposed to a bad destroyer, it's supposed to be a cheap destroyer, and I think it achieves that quite well. As for the armour, you can easily look at how durable it is in-game by clicking it in the refit screen (just like any other module) and seeing its stats.
Manta: Everyone loves the Manta, definitely give it a proper try. It's that one ship everyone looks at and thinks "this looks like a pretty weak destroyer" and then they fly it and their opinion completely flips. Glad you like the pirate version though, that thing was a joy to get flying with the Red Arrow's system.
Seraphim: I think you overestimate its defensive capabilities. If you put an offensive weapon in the medium turret, it's only got four smalls (pretty standard for a destroyer) for point defence, and they have odd arcs with the only real convergeance in the rear. I honestly wouldn't know what to give it other than Active Flares, it fits the ship well and actually isn't that strong when you consider what else it could have had, like Fast Missile Racks or something equally dumb. XD 0.6 comes from its high-tech origins, though it should have lower base flux stats than others due to smaller guns. I'll double check those though.
Gemini (Civ): Who said we needed it? I just wanted to make one.
The current Gemini often feels like it's a military ship trying to be a civilian ship, or vice versa, I just gave it a helping hand.
Seriously though, it was a surprisingly popular concept, and is different enough to the regular Gemini to warrant existing. It's also much cheaper, and has the option to install Militarized Subsystems that the regular Gemini doesn't, so there are definitely reasons to use it.
Not even gonna both with the Gypsy Moth.
If you've faced it, you know all you need to know.
Harrier: It's an anvil in the sense that it moves pretty slow. It's only really classified as such when you compare it to other midline cruisers, which are generally agile and use quite mixed weaponry. The Harrier has a single large turret and much lower mobility stats, but also improved armour and that sweet shield - it's sorta like a low-tech/midline intermission ship. It's definitely meant to punch, but the anvil part is due to it requiring ships come to it rather than go hunting for them, if you see what I mean.
Retribution: AAF on four Composite mounts is the exact same reason the Outlander has HEF on a large Synergy: it's a balance measure. Missiles are inherently powerful for their sizes, so giving a ship multi-type mounts but a system that boosts the non-missile type I feel is a sensible way to discourage memey loadout designs and usage. It's definitely a tough ship, but it really needs that boost from AAF to compete with other cruisers for firepower. Without it active it falls short due to its relatively light weaponry.