I asked the same thing on friday here: https://www.gog.com/forum/shelter_series/shelter_2_has_been_updated

As you can see, the timing for asking this is currently a bit bad, given the weekend/holidays. And since there's no guarantee he'll get the information before time runs out, here's my conclusion:

The two Shelter 2-offerings are a glitch/mistake. See, when you click on the "normal" Shelter 2, you can select the "Special Edition Upgrade", which then tells you on its own page, that it requires Shelter 2 to play.

The "Shelter 2 Special Edition" site meanwhile has no such remark. Furthermore, the "Upgrade" costs 1,79 €, which when added to the regular price of Shelter 2 (13,49 €) leads to the regular price of the "Shelter 2 Special Edition" of 15,29 € (15,28 € to be exact, but who's counting one cent?).
Lastly, the only thing the "Upgrade" adds to Shelter 2 is the Soundtrack which is precisely the only difference between the product description of Shelter 2 and Shelter 2 Special Edition.

So I'd say that you DON'T have to buy the normal Shelter 2 if you plan on getting the Special Edition. My guess is they wanted to list Shelter, Shelter 2, The Special Edition Update and Shelter 2 Mountains and whoever was responsible for putting the list up accidentally linked the Special Edition full version instead.

Granted, this is just me using logic and some deductive reasoning, so if you want to be a 100% sure you can wait for the official answer but if, like me, you don't want to take the risk of the offer running out before that, this is my suspicion.

And if it turns out to be some kind of mistake, I'm pretty certain that you can talk with the gog-staff about it.

i just purchased shelter 2 se, it includes the game itsself. after purchase i also own shelter 2.