Of-course, it is completely practical to build K-3D plugin modules using any development environment that suits you, including autotools, Eclipse, XCode, MSVC, etc. In these cases you will want to study the CMake files included in the K-3D sources to see how plugin modules are normally built, along with their header-file and link dependencies. In particular, you will need to become familiar with the K3D_BUILD_MODULE, K3D_BUILD_NGUI_MODULE, and K3D_CREATE_MODULE_PROXY CMake macros in k3d/modules/CMakeLists.txt.
Note that the binary name for a K-3D plugin module "foo" will always be "foo.module", regardless of platform (i.e. there is no ".so", ".dylib", or ".dll" extension).
When creating plugin modules in this fashion you will have to provide your own mechanism to install your modules to the directory from which K-3D loads plugins.