I started my developer career on Lotus Notes 4 back in 98. It offered a real platform at a time when web applications weren't exactly trivial to create. You could easily build database driven applications and deploy them instantly to the entire organization.
Lotus and Domino were very forward looking products. I know the conventional wisdom from users is that they were terrible, but I'll always have fond memories of working with the technology.
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.
I've still been developing for Lotus Notes as a side job during my studies - it's still very big in Europe. Developing, administering (and to some extent using) classic notes applications is still a breeze. The reason why it's so hated is most probably the direction IBM took it in. It should have neve been marketed as a messaging application. Imagine a megacorp buying Evernote and turning it into an Messaging client - that's basically what happened from what I get. The 8.x eclipse made everything worse by adding another layer on top of the old C libraries and not replacing anything. It also broke the old mantra of 'everything is a notes db/document' which is a major point of why it worked so well together - similar to Unix.