I've raided 3 end ships with no elytra in the frame, and no shulker in the treasure room. Only two people in my realm, and neither of us have raided these before.
Seems to be random, as I have found a few with elytra and a shulker, still rather quite annoying though.
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Your game is modified. It also appears you're playing on a multiplayer server, which probably means some other player has killed the shulker and took an elytra.
Seed and coordinates.