still experiencing this in the latest revision

You're running both Shagu and Questie? That's not supported. Shagu does insert things into the tooltips. What I had you turn off above is an Extended QuestLog option not Shagu. But EQL3 does come with Shagu and it's been modified from the original so I can't guarantee compatibility.

Turn off the tooltip settings in EQL3...

Maybe this is a shagu issue again? :/

Okay I switched to the supported EQL3 3.6.1 and I still get this issue

Can you send me a copy of your !Questie.lua and AddOns.txt files from your WTF directory?

After some testing I figured out that this only occurs when I have the TheoryCraft addon enabled for some reason

That kind of makes sense... TheoryCraft does it's own tool-tip injection. I've never run it and have no idea how they implemented it. I did track down a bug in Questie's tooltip code and it's related to quest items specifically found outside of a mobs drop table or a mob itself as a quest objective. Items contained in something. Not sure if it's a unique quest item or not as I was only able to re-pro the issue once but I did confirm a specific block of code that it's looping through twice. I've pointed it out to the original contributors and am getting their feed back on it before I attempt to write a fix. This block is in a function that has several situational checks in it and I'm not 100% sure what they all do and I'm afraid that I might break or introduce a new issue so for now I'm leaving it alone.

This will be fixed in version 3.1 which I'm preparing to release now.

Im still getting the duplicated quest drops while running TheoryCraft v1.06.5 and Questie v3.1 together.
Quick fix is to edit TheoryCraftTooltip.lua in the TheoryCraft addon and remove line 46.
I just changed

end
frame:Show()
return frame

to

end
--[[frame:Show()]]--
return frame

All the tooltips seem to still be working properly for me.