I have shift-selected a subtool in the subtools menu and now all other tools are masked. That’s not what I want since I want to merge all visible subtools. This won’t work with a number of subtools masked. CTRL-SHIFT-A (unmask all) doesn’t do the trick. What does?
You are probably not seeing masking, but rather selection highlighting. Inactive subtools appear darker than the active subtool. You can only mask/unmask the active subtool.
Masking will not prevent Merge Visible from working, but the resulting new tool in the tool palette will retain that masking.