LittleSnitch for Mac is a good looking app.

I always thought that ugly UIs on Linux are because of good designers do not intersect well with programming enthusiasts.

But looking how ugly same app looks on Linux, I’m starting to think it could be a technical limitation. Can someone elaborate?

It just depends on the UI frameworks available to developers and their interest in building something good-looking. Different UI frameworks are available for different platforms, and there are only a few good ones that are cross-platform. Qt and GTK are pretty common for linux apps and typically don't look great.