I assume yours was a rhetorical question?
Well, I assume your answer as to which makes more sense would probably match mine. I do think it's a fair argument to bring up, though, and I didn't see things put in those terms elsewhere.
I would expect that owners of large herds of cattle would probably want to chip their animals to aid in tracking changes in weight, food consumption, etc. Someone with three cows, however, may prefer other means of identifying them (e.g. this one's Bessie, this one's Danielle, and this one's Phyllis). Such a person would have little use for an implanted microchip (except, perhaps, as a slight anti-theft measure).
I can think of plenty of bad uses for the NAIS database; it's hard to think of good uses that couldn't be accomplished just as well by letting people keep track of their own livestock.