Based on the updated immiigration information as of sept 2014, it looks like nepalese passengers do need transit visa while in transit. Go to the following honkong's official link n scroll down where u see a table where it says visa required for nepalese passengers even on transit.
http://www.immd.gov.hk/en/services/hk-visas/visit-transit/visit-visa-entry-permit.html#notes