That's how it looked like to me as well. I loaded it into Vim in the hopes of attempting an edit (regex search / replace), but the structure was too convoluted in terms of the file itself. Besides I didn't see anything in the registry itself that looked likely, so I probably wouldn't know what to change even if I could reliably do it in the file.
No matter - I was listening to some music last night while I just plodded through each and every item, manually changing each one.

...probably because it was Friday night and after this week at work, that level of intellectual endeavor was about right for my tattered mental state.

The settings are kept in the workplace preferences, but I didn't see anything likely in the registry. Loading a different workplace affects their visibility.
I noticed if an item appears twice (e.g., in a stock menu as well as a custom one), changing one took care of both. I suspect they're implemented as one struct (or class) per item with pointers to it for duplicates. Setting the icons to visible also revealed a design flaw in the menus themselves: For toggle items where a check mark appears when enabled, the icon now covers the checkmark. Those two functions need to be separated somehow.
Related question: Is there a reference for command line parameters? Specifically, can I set the workplace from the command line (i.e., have different icons for different layouts)? I've Googled but found nothing so far.
Thanks.