My sense from friends and colleagues who have used or developed for Lotus notes is that Users generally hated it but people developing apps for it loved it. I've always assumed the technology was solid but like most things in the category of custom one-off but long lived software for companies the UI/UX was almost always subpar.
I think you nailed it. Notes apps that aren't developed with some strong UI guidelines tend to look ugly. It's a bit like web 1.0 in terms of UI - good developers can make neat and useful applications with it, but most of the stuff just looks bad since useful guidelines weren't there yet when the tools have first been developed.