When a shulker is spawned it will face south, this continues to be the case after going into minecarts and ejected using an activator rail into the central exit portal in The End, as expected it appears on the world spawn location.
Transporting it again via minecarts is not an issue, ejected shulkers still face south.
However, once the shulker is transported through a nether portal while riding a minecart and then ejected it will face WEST, this can be confirmed by placing the shulker in a boat and using F3-b to show the hitbox.
This causes shulker teleportation to change which breaks a lot of farms.
The rectification to this is to realign the shulker after going through the last portal using a boat and rotating it to face south as when it was spawned.
I cannot reproduce this, for me the shulker is still facing south, as expected. Could you attach a video or some screenshots please?