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instead of setting hasmain to '0' in xoops_version.php you can achieve the same effect (omitting them from main menu) by setting the module weight to 0 in System -> Modules.
I was not aware of the dependancy of the Module Group Permissions being tied to the hasMain property of a module, but I'm sure there is a good reason why. Perhaps the effect is not direct, but hasmain is used for another property, which is used for the group permissions page.