It will load them from PK3s if your directory structure is properly set up. It will also have a feature to load textures from a directory or treat a directory as a PK3's root.
I know Doom Builder can do that, but can it load textures from folders inside a zip/pk3 (GZDoom requires that all hi-res textures be put into a Graphics\ folder within a zip/pk3 -I also have further nested directories in this zipped Graphics\ folder.)