The bug
Bee nests and hives are copied with a outdated honey levels, when ctrl-pick-block is used.
To reproduce
Switch into Creative mode
Place an empty bee nest or hive
Adjust the honey level with a debug-stick, or wait for a bee to raise the level
Press
Ctrl
+Pick Block
Place the new bee nest/hive somewhere else
→ ❌ The newly placed bee nest/hive is not full of honey
Alternatively, breaking a nest in creative will generate a placeable copy of the nest with the correct honey value, but placing that nest and ctrl+picking it again, will always generate a nest with that new honey value, even if the level changes between placing and ctrl+picking.
Related issues
is duplicated by
relates to
Attachments
Comments

This is related to block states, not NBT. I'm not sure whether Ctrl + Pick Block is supposed to copy the block state at all.

same problem
Doesn't seem fixed to me in 19w36a

Can confirm that it's still an issue in 19w36a.
It only works when you punch the block in creative. The level will still be kept, even at the max level.

Is it really an issue? The honey level is a block state and ctrl+pick block only copies NBT data.

This bug would be invalid, because you could modify the block state with a debug stick.
But also this bug would be valid, because honey levels are affected on normal gameplay, so their values would be retained by Ctrl-Pick command.
Conclussion: This is Mojang staff decision. They would choose the best option.
Can confirm in 21w05a.
Can confirm in 21w05b.
Can confirm in 21w07a.
Can confirm in 21w08b.
Can confirm in 1.17.1.
Can confirm in 1.18.1.
Can confirm in 1.18.2.
Can confirm in 1.19.2.

can partially confirm in 1.21 full release.
The behavior seems to now only apply to full honey blocked placed with /setblock, potentially other force place methods(i did not test those)
However once i BROKE the block in creative, dropping the item, and then placed and picked, it did correctly copy and place with the data. My guess is some behavior has been fixed by item components, as picking after that process would properly copy the component, but force placement NOT using components cannot be picked.

Using a debug-stick to change the honey level seems to have the same effect as set-block, that is: Setting a hive to full with a debug stick, will create a honey block that will behave differently when ctrl-clicked than if it were first broken and replaced.
I cannot be sure when the behaviour changed, as I had been using a sticked hive for testing.
Edit: This doesn't quite seem to be quite complete. If the block is adjusted by a debug stick, or indeed by a bee, then ctrl+pickblock will behave as though the adjustment never happened. The only case where it preserves the honey level is if the block was broken and replaced in the way you suggest.
I will update the report