The possibility for a third party plugin to remove the standard Squeezeplay menus seems to have been removed in Jive.pm in this change:
http://svn.slimdevices.com/slim?view=revision&revision=27529

Was this the intention or was it done by accident ?
(The svn log comment "There is probably more work required in this area." seems to indicate that it might have been by accident)

I used this in the Custom Browse plugin to make it possible to hide or replace standard menus inside "My Music". I don't think it's possible to remove individual items underneath "My Music" with the "Home Menu" in Squeezeplay, so that's why I had the possibility in Custom Browse.

The correct way to solve this would be to fix the "Home Menu" configuration so it's possible to hide also items underneath "My Music" and not just the items in the "Home" menu.

Some samples of bug reports that is related to more flexible menu configuration:
https://bugs-archive.lyrion.org/show_bug.cgi?id=3817
https://bugs-archive.lyrion.org/show_bug.cgi?id=9358
https://bugs-archive.lyrion.org/show_bug.cgi?id=10056
https://bugs-archive.lyrion.org/show_bug.cgi?id=14004

However, unless that's possible, is there any way to bring back the possibility for a plugin to call Slim::Control::Jive::deleteMenuItem with one of the standard menu identifiers ?

At the moment I can make the call but it doesn't save the result so the next time Squeezeplays retreives the "My Music" menu the server returns the whole menu, also the previously deleted items.

There are a number of other bug reports regarding more flexible menu configuration, so if you choose to go that route instead of the programmatic route suggested in this bug report you can close this report with "Won't fix". 

There are two situations where you like to remove/override menus:
1. You want to remove menus you don't use to make the interface easier for kids or other people who get overwhelmed with having a lot of browse menus.
2. You want to replace one of the existing browse menus with a menu from the Custom Browse plugin.