Some people have asked this question before and I don't think we had a definite answer. Found this article (thanks to Reddit) about The Taken King pre-order and it says the physical versions will come with digital codes for all the expansions. We suspected this, but it's good to get confirmation.

Also for the stuff they mention about "Coming Soon" or "Unavailable" showing in the PSN/XBL stores for the digital versions, make sure you are logged in on the site before checking.