Its worth mentioning that nvenc is an encoder that uses the GPU on the graphics card not the CPU. GPUs are massive parrallel processors capable of processing graphics in a fraction of the time as the same algorithm on a CPU. Using h264_nvenc will only affect the the library used to encode frames into the output video file. Decoding source video files into frames and applying affects those frames may still be performed on the CPU.
When I’ve discussed this elsewhere on other forums for other products (including lightworks) the reasoning given was that entirely GPU based systems are generally propriety, non-portable and hardware dependent (isn’t nvenc only for nvidia cards?). I can’t speak for MLT and shotcut but whatever the reason exporting is CPU bound. There are features which use the GPU if you switch them on, but there’s still a lot of CPU work.
For simple transcoding you can find ways to do this entirely on the GPU. I believe you’ve found one with ffmpeg and nvenc. But I’m not aware of an NLE which is entirely GPU based for exporting. They’re simply not designed that way at the moment.
So in short, your processing times sound about right, and I don’t believe you’re going to do much better with alternatives to shotcut if you want it as an editor and not just a transcoder.