As far as can be seen, yes sadly, they are. Some of those were preorder bonuses for ARR and Heavensward, while some were codes with the first runs of certain merchandise (Bluray soundtrack albums, artbooks and plushies). All these items the codes are limited time to both acquire and register - they actually have a useby date so even if you track the codes down after a certain time, they will be still unattainable as the time to redeem them has passed (this is the case with the Wind-up Dalamud at least - the code for that expired on December 31st 2014).

And as the only items that have appeared on the Mogstation for purchase at a later date have been only items that were available for free in the game during limited time events and not ex merchandise items, I really don't see things like the Wind up Dalamud ever appearing on the Mogstation I'm sorry to say. That's not to say SE that there is no chance that SE will change their minds, there is always that possiblity. But the most realistic outcome alas is sadly those items are gone forever I'm sorry.