Might have something to do with the fact that I can't shake the feeling that a lot of them are unbalanced
i know the feeling, and there are some popular mods i don't use for that reason. overpowered stuff kills the enjoyment for me, because it removes so much of the choice and variety in fleet composition or loadouts, not to mention making the game less challenging (if the enemies aren't using overpowered stuff as well).
but i remember initially having that feeling with some of the actually well balanced mods as well, when i first started using them. there are many ships and weapons that look quite a bit stronger (or weaker) from a quick look at them than they actually are in practice, because there are so many things in this game that influence how well a ship or weapon does -- and some of these things aren't even shown in stats at all, like projectile velocity. a ship/loadout may seem really powerful for a few battles, until you run into an enemy fleet that counters it. and some ships and weapons just don't have any vanilla equivalent at all, so it can be hard to judge how well they're balanced.
keep in mind, vanilla itself has massive differences in power/usefulness between its weak & cheap ships and weapons compared to the really good ones. so if a mod ship or weapon does something better than a vanilla one, that's okay, if it's intended to fulfill a rather specific niche or has some drawbacks (which might not be immediately evident) that still keep it from always being the best choice.
Underworld, Ship & Weapon Pack, BRDY, II, THI, SCY, DA, SRA and even Templars are all pretty well balanced. not
perfectly (nothing is ever perfectly balanced ^^), but well enough to be in line with vanilla, and several of them are currently getting big updates to further improve this. :]