So I have seen the same question asked on 5 different stackexchange sites, and all the answers say to just remove the hotkey, which does work, but isn't the root of the problem (at least it wasn't for me). The real problem is that the windows super key is not mapped correctly, as is described here:
i3 ignores mod4 (windows key) when in VNC session
Basically just run these two commands
xmodmap -e "clear mod4"
xmodmap -e "add Mod4 = Super_L"
That should do it. Now the desktop should only be shown if you hold down the super (windows) key as well. The "d" key (and other keys with super shortcuts) should now work as expected.
You may need to replace Super_L with something else depending on your keyboard, check the link above for details.