In late 1985, the first run NES systems were test-marketed in limited scope in just a few major US cities. I don't have information offhand about the cities it was released in but the number was rather small, as the USA Nintendo operation was rather small at the time. It wasn't until 1986 that Nintendo of Japan noticed a re-emerging industry in the US and decided to give USA Nintendo the go-ahead for nationwide distribution with the new stock of units, which were the common gray-button variety that they stuck with until production of the original design was stopped. What I'm not entirely sure about though was the decision to make the change...the timing of the Zelda commercial would probably clarify the issue though...since it was released in 1986, it's very likely that the black buttons were changed as a result of the US test market.
And yes...the black-button version of the NES is extremely rare...they wouldn't make up even 0.01% of all the NES units manufactured. Considering Nintendo's claim of over 60 million NES units produced during its lifetime, and the first run being a very low number for a first-run console (I believe it was actually under 5k units total)...good freakin luck finding one at all, let alone a minty fresh one.