I'm confused about the rationale for removing any of these optional mods. They're optional, so keeping them isn't interfering with any playstyles preferred by the devs. Do they do anything when not active*? Because if they don't than there's no instance when devs who don't like or deal with them would have to actually modify them. If a player who uses the mod notices a bug, they can fix it themself - open source yay - or find someone else able and willing. Regardless, keeping these options in the start-game mod menu makes them available for those who like playing with them, and doesn't affect those who don't. Removing them is not a solution relevant to devs not wanting to be burdened with maintaining them. Just keeping them in the start-game option list requires no maintenance. Their original creators can maintain them. If those are gone, voluntary interested supporters/devs can volunteer. If none show up, the players who like the mods can figure it out (yay open source.) Removing them just makes the game less flexible and solves no problem.
* If they do and this actually creates bugs in non-backwards-compatible new systems, and no one is going to maintain the mod in question, remove away. If the mods aren't doing any damage, they are optional, and any portion of players like them, keep them.
Also, what's this about filthy clothes? Are filthy morale penalties being mainlined, or a no-filth mod removed, or both, or something else?