Spock was the only alien we saw, there were likely dozens of others onboard that kept missing the camera. Its the same way we never saw a stellar cartographer in TOS but you assume that a ship of exploration has several.
You can make any assumptions you want in order to justify anything. But the fact (what we actually saw on screen), was that the 1701-Ent had one alien in it's crew. For the NX-01, a ship which was launched some 200 years before the 1701, and a pre-Federation ship, it was perfectly natural for there be only one alien. In fact, if Archer had had his way, there would not have been any. Considering how xenophobic humans were in the 22nd century, this seems logical.
ENT as a Earth-based ship makes sense to have few aliens onboard, but it should have been an early Federation ship instead with lots of aliens on the crew.
Why? Ent was a show about Earth's initial exploration outside of the solar system prior to the formation of the Federation. You may have wanted
to see an early Federation ship, but other than that, I see no reason why Ent or the Nx-01 "should" have been about the early Federation.