This has been happening at least since 4.2.8, probably longer. I just didn't connect things until now. STEPS TO REPRODUCE 1. Observe how right-click on vector layer or with the reference image tool enabled gives you the vector context menu 2. Go to Settings -> Configure Krita -> Canvas Input Settings -> Show Popup Palette 3. There's an existing keyboard shortcut there. Edit "Mouse Button" to "Keyboard Shortcut" and leave "Input" at "None", then save the settings. 4. This will disable the popup palette on paint layers. However, it will also disable the right-click vector context menu. (Right-click context menus on other parts of the GUI than the canvas, e.g. in dockers, still work.) Code-wise I can see why this happens—I guess that the popup palette *is* the context menu on paint layers. However, the settings option lead me to believe the shortcut was only for the popup palette and that I could disable the popup palette and only the popup palette. Which is a feature I very much like to have.
Yes, this is sort of expected... Maybe we should rename it in the canvas input settings to "Open Context Menu" or something like that. Trying to separate the two actions is going to be a lot of hassle.
OK. I guess I'll find another key to rebind it to that doesn't get in the way as much. "Open Popup Palette and Canvas Context Menu", maybe? People will be searching for Popup Palette since I don't think it's clear to a lot of people that it's a context menu, and "Canvas" should be in there because it doesn't affect context menues in other parts of the GUI.
Resolved as of Krita 5.0 (I believe), commit b1bf3453 !