I find this feature annoying more often than I find it useful. For example if I want to test something with only a single mod and temporarily disable every other mod I would just take all the current mods and throw them into a different folder. The easiest option would be just a subdirectory within mods called like "disabled" and then take them back out of there later.

I don't know if anyone at all uses the subdirectories feature at all. I assume it's there to allow better organization but it actually prevents me from organizing mods how I want (right now I need to put a disabled mods directory OUTSIDE the mods folder which gets kind of annoying to navigate).

A good middle ground would be to have some way to specify a folder shouldn't be searched by the mod loader so for example a dot. That way I could make a folder called ".disabled" and anything inside of there would be ignored, but also I think completely removing this feature is a good option, unless there are actually people who use that to organize their mods.