I don't think it's a SSD vs HDD situation (both should work perfectly fine with any DE) but rather a case of old and dieing HDD, that's at least what caused my system to fuck up two years ago or somethimg like that. There are systems that work better on far slower than HDD (today only "achived" by dieing HDDs) speed tho so I could imagine that improving the situation, just don't sotre important stuff on that till you got a new drive!
htop, distrobox and in some cases Flatpak!
Edit: after reading the comments I want to add curl and git, seriously, why aren't those a default?!