We wanted to take a moment to clarify that the extra elemental damage from weapons such as Thunderfury, Blessed Blade of the Windseeker, Iceblade Hacker, and Warblade of Caer Darrow are behaving as expected in WoW Classic and do not actually cause additional non-physical damage to the target. They do however still inflict extra damage in the amount specified in the tooltips. This is not noted in the combat log separately and is simply calculated as additional physical damage added to the weapon’s attack.
That being said, it has been noticed by players that when using an elemental barrier such as a nature/frost/fire protection potion or a shield that absorbs a specific element, you will see an “absorbed (X)” message in the combat log. This is also correct and working as expected, and such effects will reduce the damage of attacks by such weapons by the amount of extra elemental damage specified in the weapon tooltip.
Ultimately the way these weapons function is a very old quirk/bug with how original World of Warcraft was built. While definitely strange and unintuitive, these weapons are behaving exactly as they did in the original game and we have no intention of changing them to behave differently in WoW Classic.
I hope this helps provide some clarity around this very odd quirk inherent to these types of weapons!