Mark of the Ninja Remastered (free for Special Edition owners)

And I can't buy the old DLC as it is replaced with the new version.

Actually I think you can in a sense because the old Special Edition DLC and the 'new' upgrade to remastered version seem to provide the same thing from what I have seen. This is both backed up by the database entry for the upgrade package on steamdb as well as an old Steam gift I have in my inventory for the Special Edition DLC. In both cases they list Mark of the Ninja: Special Edition DLC (app 239570) and Mark of the Ninja Remastered (app 860950) as being provided.

As to whether Klei will now offer that package on sale since it gives the remastered version of the game is another story. Like you said they could see it as a special offer (since it serves no other purpose as it not being sold as the SE DLC for the original game even though it appears to give it) and decide not to discount it. Who knows. I guess we will find out in a few months. You could certainly end up being right though. They are stingy sometimes when it comes to discounting DLC. Been waiting for what seems like forever for a higher discount on Shipwrecked DLC for Don't Starve for example.