I am facing the same problem which was reported earlier in issue JENKINS-4561.
My Hudson version is 1.361.

In my case, the option "Delete All Disabled Modules" is visible for users but they are not able to delete these modules even though they have delete privilages when project-based security is enabled. In top of that, privileged user can use the option above, if he will enter manually URL similar
to this one: http://hudson-installation/job/the-project/deleteAllDisabledModules