Valve rarely replaces old games in your library for "new" ones, instead they add the new one and just remove the old one from the store. So you wind up with say Arkham City and Arkham City GOTY in your library. (When WB only patched the later to get rid of GFWL, they gave it to everyone who had the former.) Company of Heroes I have the original game, and all its expansions, and then I have the Steamworks version that has all the expansions included. The two recent Dead Island Definitive Editions replaced the old games on the store, but the old games remain in my library. So on.
I think if you currently buy the Legendary Edition it's a separate entry as well, like the Deus Ex HR: Director's Cut and a number of the GOTY versions of games are. Dishonored I think.
So I suspect it'll be a situation where if you bought everything, you'd wind up with:
Skyrim (with all the DLCs)
Skyrim: Legendary Edition
Skryim: Special Edition
This is one reason when the new Complete/GOTY/etc. versions come out, the old DLC gets shitty or no sales. Or there's situations like GTA IV where you literally couldn't buy the DLC only (and it was never on sale) because Valve and Rockstar forgot they replaced GTA IV in the store with the Complete Edition so when you went to buy it, it'd say you own it already. (Which IIRC, the Complete Edition shows up as two separate titles, GTA IV and Episodes from Liberty City, in your library anyway because it was just the store that was changed.)
Valve's actually the primary company that just replaces their games, the original version of Half-Life 2 isn't downloadable from Steam anymore. The version now is the one ported to a later version of Source which changes some effect or maybe the timing on something speedrunners use. There's probably a list somewhere.
