Shulkers will only apply their natural armor after opening their lid and then closing it again.
Steps to reproduce:

• spawn a shulker
• wait for it to open its shell and close it again
• hit the shulker with your fist
• observe with the command /data get entity @e[type=shulker,limit=1] Health that the shulker now has 29.78 health, showing that the natural armor is working
• kill that shulker and spawn a new one
• hit the shulker with your fist again, but this time make sure you hit the shulker before it has a chance of opening its lid
• observe with the same command as above that the shulker now has a health of 29, showing that the natural armor is not working, even though its lid is closed

(this effect can be more clearly seen by using a weapon instead of a fist)

Expected: shulkers always have their natural armor applied if their lid is closed

Observed: shulkers do not have their natural armor applied when newly spawned in (also probably effects duplicated shulkers, but would require a more complicated setup)

(Edited for a simpler setup to reproduce)