NGUI's clipping is done by simply finding a similarly named shader -- for example "Unlit/Transparent Colored" will get "Unlit/Transparent Colored 1" when clipping is needed. It's actually an old way of getting shaders, and I've been meaning to change it into a single multi-compiled shader, but never seem to get around to actually doing it (mainly because of the "it works, so why mess with it?" excuse).
If you create a custom shader, make sure to also create the clipped versions of that shader that will follow the NGUI's expected naming convention.