This was fixed upstream by commit bc9b012 ("Add a Science category to the
menu. (#12215)", 2024-05-31), which adds the cinnamon-science.directory
entry, the Science menu section in /etc/xdg/menus/cinnamon-applications.menu
and excludes the Science category from the Education menu.
The fix is in upstream Cinnamon since 6.2.0, and in Debian since cinnamon
6.2.9-1. I verified it on the binary packages currently in the archive:
both cinnamon-common 6.4.10-2 (trixie) and 6.6.9-1 (unstable) ship
/usr/share/desktop-directories/cinnamon-science.directory and the
corresponding <Menu><Name>Science</Name> section, so applications whose
.desktop file declares Categories=Science are now listed in their own
Science submenu instead of falling back to "Other".
Bookworm still has 5.6.8-1 and will keep the old behaviour.
Thanks for the report.