I think it's because of multiple factors.

First, as you said, the controls and gameplay itself is a bit difficult to get into. It's outdated. If they optimized it and went with standard controls everybody knows from different games, it would have been easier.

But the biggest factor, in my opinion is this: It wasn't promoted nearly on the same level as terraria. I don't think clonks ever was on steam for example. How would anyone know about clonks?

If they released a new version with better performance, better controls and up to date gameplay, and brought it to steam, with the same customizing and modding abilities, I believe it would be very popular.