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There is no 64-bit version of Notepad++, as of vTemplate:CurrentNpVersion. So, on a 64-bit operating system, what is installed is a 32-but application. That's the stem of it all.
64-bit editions of Windows know how to tell the CPU to run 32-bit applications like Notepad++. Such systems can deal with them as well, but in compatibility (read legacy) mode.
Because of this, Notepad++ and its plugins can only use GUI elements that exist for 32 bits to use, not the ambient theme. Even having 64-bit dll's won't help, because they will be run in compatibility mode. WoWW64on32 will be able to put the CPU back to 64-bit mode when accessing such extensions. Windows doesn't like such mixed constructs - nor does it like alien stuff altogether.