We have a duplicated menu in antiX as well. Specifying all of the submenu (<menu></menu>) blocks in the applications.menu file as <Menuname>Block Name</Menuname> instead of relying on <Merge type=*.... stops the duplication.
It seems as though this is an upstream bug from pyxdg almost 2 years ago. Reported issue https://gitlab.freedesktop.org/xdg/pyxdg/-/issues/11 Merge request / suggested changes. https://gitlab.freedesktop.org/tmccombs/pyxdg/-/commit/087410c64fd4d6db1ec2d70aa196e69b25c887eb
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