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Officially there are no longer any restricted areas in Nepal. The immigration office rules now state that "trekkers are not allowed to trek in the notified areas previously known as restricted". Rather than get involved in all this semantic complication, the term "restricted" is used here to refer to places that are closed to trekkers, or open to trekkers only when accompanied by a policeman.
There are many reasons why the restricted areas exist. In most cases, Environmental groups, particularly the Nepal Nature Conservation Society, are pressuring the government to keep some places closed for ecological reasons to avoid both cultural and environmental degradation. Because trekkers require assistance when something goes wrong, the government restricts some areas because it doubts that it could provide the security that trekkers need. There are also political reasons for some restrictions. In the 1970s, for example, the Jomsom trek was closed because a major foreign-aided military operation had been mounted there in support of the Khampas in Tibet.
There are many influences on the decision to open or close certain parts of Nepal to foreigners. Recent changes have liberalised both trekking and climbing, and there is considerable pressure to open more areas to trekkers. You should check with a trekking agency or the central immigration office before planning an unusual trek.