Source code for latest version of ndisapi with a couple of new samples is now available on Github. I’ve just tested dnstracer with and and without WinpkFilter driver installed and availability of the driver was reported properly (so the calls to CNdisApi::IsDriverLoaded worked correct).
What was the Windows version you have tested? I’m not sure, but if you use NCF_HIDDEN attribute for your driver build then it may also affect netcfg output.