I haven't used Qt or GTK with Node, so I can't give any recommendations there...
There may be some alternatives: it looks like there are bindings for wxWidgets, OpenVG and some OpenGL-related libraries (GLFW, GLEW and SDL). Though OpenGL is typically used for 3D, my impression is that it can also be used for 2D. I doubt there are mature widget libraries for OpenVG/OpenGL implemented in node, but you might be able to write bindings for one in C++. If you're targeting a single platform, it may be simpler to look for node bindings to the native platform API which should provide native controls.
Node isn't strong in the area of native desktop apps - not that there are inherent problems, but these aren't a strong focus for the community at present. Perhaps this is partly due to Node's async leanings, which are very attractive for a server that may need to scale to thousands of simultaneous connections (at least in the wildest dreams of the developers), but just adds unnecessary complexity for desktop apps.