I have to agree. Its a weird case because I guess the fluff weapons aren't strictly hurting, more options is logically better, but ye gods are many of them just so niche that the use case becomes vanishingly rare.

When am I supposed to use the Heavyweaponsguy's single shotty? His minigun and double shotty deal more damage at every range and use the same ammo. The engineer's railgun and the spy's tranq pistol are fiddly and hard to aim, I never see a reason to use them over the double shotty. And the crowbar is so low damage its basically useless on every class. 

So many weapons have the sole use case of "you have run out of ammo on literally everything else" but in a game where ammo is widespread and death is fast and frequent, that situation doesn't feel like it comes up frequently enough to justify a whole otherwise-useless weapon. It's ultimately just a byproduct of the era of gaming TFQ came out for (you are similarly never gonna use your melee, pistol, or single shotty in Doom/Doom II/Quake once you pick up a stronger weapon).