I'm willing to bet that Nightstalkers were developed there, but we already know how Deathclaws came about. They were created by the US military before the war by applying FEV to Jacksons Chameleons.
We may already know about the deathclaw's origins, but we also already know that nightstalkers are just coyotes and rattlesnakes spliced together. Doesn't mean the Big Empty wasn't the facility that created them both.
I'm going to guess that escaping from the Big Empty requires us to deactivate the entire security system, allowing new breeds of nightstalkers, deathclaws, and perhaps new creatures (wanamingos) to roam the Mojave.