From what I understand the mods being removed are because they no longer have a maintainer and the cost to keeping them updated is higher than the current dev team can spare while trying to add new features and improve the game. Naturally, those mods will not likely make a return unless somebody is willing to dedicate to keeping them updated and functioning.
I believe another issue was that many of the core team don’t use a lot of the mods that are up for removal and so it wouldn’t make sense for them to do updates for those mods because they are not part of the intended audience.
SOME of the mods might still work but you have to remove the obsolete flag from your local copy and keep it with you because it won’t be served with the main game anymore, Erk has an answer in another thread similar to this one
The Issue on GitHub being discussed:
Guidelines and Information on how Mainline mods will be handled going forward: