Taking the "NCR" location in Fallout 2 as Shaver Lake, the distance to Navarro is only about 275 miles. And the NCR in Fallout 2 wanted it's fingers in many distant pies, including New Reno, Vault City, and putting pressure on slavers well north of Navarro. Wiping out a major likely competitor would be just the kind of thing NCR might try. Remember, they have their positive side, but also a negative one...and could easily fall prey (through ambition or arrogance) to the vicissitudes of imperial overstretch.
As for the NCR being too far away, I'm assuming the NCR of 2244 would have had a military base near Bakersfield (Necropolis) that it would use as a base to launch an operation against the Enclave at Navarro. From Necropolis to the real world town of Fort Bragg (No actual fort is there) is 440 miles or so, depending where along the coast Navarro's location would correspond to.
Even if the NCR went as far as Fresno, the bulk of its military would likely be farther south and closer to home rather than on the frontier. I say this as some one who plays Civilizations a lot. Strategically, it is better to keep your military closer to your homeland than it is to keep them on a far away frontier. Yes the NCR would have had troops all the way up to its northern frontier, say Fresno, but there would only be enough troops to perform the local mission. There wouldn't likely be enough to launch an invasion, except as a stop over point for the force that assaulted Navarro.
As for influencing towns outside of the NCR and hundreds of miles away from its territory, ever nation can do that. The US can put pressure on any country it wants, whether or not invading makes any sense. Or like before WW2 we had economic power to exert on others, like the NCR has. The pressure seemed more economic in Fallout 2 rather than fear of an imminent invasion. Yes they could, but would it be their first choice? And the NCR, at least from my perspective of it, is a caricature of pre WW2 America.
My argument as a list is...
1. The NCR did attack Navarro.
2. The NCR had a major military base 300-400 miles from Navarro.
3. The NCR had problems supplying the Mojave in 2281.
4. The NCR had fewer resources in 2244.
5. It is likely that the locals didn't like the NCR's invasion
Conclusion: The NCR did attack Navarro, but with logistical problems and an unwilling local populace, didn't finish the job and some Enclave personnel survived in the vicinity of Navarro.
This also leaves the potential that the Bay Area and Coastal Northern California isn't under the NCR and possibly under the Shi and Enclave. This leaves the possibility for a future game set in Northern California, since the Enclave and Shi would be hostile towards the NCR, the NCR being invaders.