I believe there was only one class that excluded fairings, it was F-RD and it no longer exists, as far as I know fairings are legal in all classes and there seems to be no restrictions with the following exception: "No brackets or bodywork shall be made of Carbon Fiber or Kevlar except in V6 and V7. Carbon Fiber silencers are allowed on 2-strokes."
The following are the only restrictions I found. No brackets or bodywork shall be made of Carbon Fiber or Kevlar except in V6 and V7. 350 GP: Honda 350cc twins with the following limitations; no fairing. In all GP classes...bodywork must be of a type actually available prior to 1972.