Hmm, I don't really use playlists or queue myself, but logically I think they should be added and kept as disabled. If someone went to trouble to manually mark tracks as "disabled" in the album's folder, it stands to reason that this choice should be remembered when you add the album to a playlist or queue. Also, adding them to a playlist will make re-enabling them later much easier because otherwise you'd have to manually add them which is a hassle.
But it does introduce edge cases, like what if you add a whole bunch of albums to a playlist and half the tracks in those folders are disabled, so the playlist is a bit of an eyesore now with all those disabled tracks. The problem is that it's a great idea for albums because there aren't a lot of tracks in an album, but for people who like using long playlists it can be a bit of an issue.
Though then again, if you're one who uses playlists you'll be adding a bunch of tracks to a playlist manually. If you don't want to listen to a track then you just won't add it in the first place. This skipping feature is relevant to those who like to listen to entire albums but perhaps want to skip a track or two. So there's not really a lot of clash between these two use cases, not that I can see at least.
The other way around - disabling tracks in a playlist should definitely not apply to folders, that doesn't make a whole lot of sense because a playlist is already a curated subset.
I don't know, it could be solved by a toggle option like "ignore disabled tracks when adding to playlist", as well as a toggle option "hide disabled tracks in playlist" to take care of the case where you have too many disabled tracks in a playlist for some reason.
Haha, this is how it always works, you think of a simple feature, but turns out it has a whole bunch of edge cases and consequences. Anyway, I'd be really happy to see even a very simple implementation that works strictly in folders with no connection whatsoever to playlists/queues if implementing this extra stuff proves too cumbersome. Like I've said, I think this feature will be the most useful to people who like to listen to whole albums and want to skip a track or two, whereas people who use playlists will likely use playlists to manually select the tracks they want to listen to, so they have less of a need for this kind of automatic track skipping (they already chose the tracks they want, after all).