The Enclave would go through Metzger because they're trying to keep public awareness of themselves limited. Arroyo was, most likely, an exception because they were making breakthroughs with the FEV and didnt have time to wait for Metzger to produce more slaves.
Also, maybe I missed something, but the idea of enslaving a bunch of Jet users in New Reno either for tests or for general labour doesnt work. Jet addictions or not, if users started being abducted and forced into Slavery then New Reno would begin to clear out pretty quickly, and the Mordino's wouldnt want slaves already addicted to Jet as you cant gauge just how addictive it is if the user was already addicted. Which is to say, theres no way to tell if theres a 100% addiction rate from one hit of Jet if you're testing it on people who are already addicted.
All that aside, you have to put things into perspective. In one of the holodisks you get in Vault City it lists specifics about all the different towns and I believe it said Vault City itself had somewhere near 1000 people. I could be wrong, but either way, no city in the game had that many NPCs. The cities, mechanics-wise, were like an abridged versions of how they'd actually be if they existed in real life. Accepting the Fallout universe on the face value of the games doesnt really do it justice.