This has been issue since somewhere Dragonflight and never figured out what was causing it but now I found it...

In Threat Plates settings:
General -> Blizzard Settings -> Display
These option do not matter, have effect or are not applied on reload.

Only way to fix this bug is to go to WoW's own options:
Esc -> Options -> Game -> Graphics -> "Use UI Scale"
- Either uncheck apply and re-apply or change it to 65% and back to 64%
After this the the Threat Plates settings:
General -> Blizzard Settings -> Nameplates
Need to be reapplied ie. if you had Enemy Widht/Height 180/25 you need to to set them again 180/25 to take effect.

Now the clickable area is correct again.

Would be nice to not be needing to do this everytime you load into instance, game or /reload.

Cheers!

Edit:
Seems like the same issue is on other nameplates too when you reload the Clickable Area breaks.
I don't think it is fixable since when you login or /reload it breaks.
Setting UI scale manually with /set command doesn't work, the fix needs to be done through settings with "Apply" and then do the set with Threat Plates that I wrote above.

Maybe you can find solution or not.

Found the problem and fix to manage with current version.

Options → Interface-> Names - > Larger Nameplates

If this option is enabled the clickable area will have additional invisible clickable area that scales along Blizzard's Horizontal, Vertical and Global nameplate scales.

Making Vertical scale smaller for clickable area will cause these boxes being separate as it seems the box above has fixed position to be higher than the actual clickable area.
Causes the issues to be able to click nameplate below another instead if the invisible clickable area is top of the other nameplate.

Making Vertical scale bigger causes the invisible clickable area to overlap with the actual clickable area but that box seems to have restricted position where the bottom cannot exceed the actual clickable area's so the invisible one keeps scaling but only more to upwards.

Fix: Disabling Larger Nameplates makes things work normally.

(im playing on 3440x1440 monitor if that has anything to do with the issue)