Essentially the things are parking lots, which can receive additional crew in the event of wartime deployment. Small craft are kept in the Nu'Fei to keep them maintained, and to ensure that they're ready when the time comes.
Additionally, after a hefty sum of banging my head against the wall I figured that the several kilometer huge interior could easily house that many small craft. However, it won't be housing 750,000 at all times, it is just a matter of slack allowing for small craft to be transferred from one assignment to another, or for affiliated/allied assets to receive aid from these massive parking lot service stations.