We only saw 3 fairies there too. We got there right at opening (by chance, not by plan) and had about a 10 minute wait. We saw Tink and Terence and Iridessa. Pixie Hollow went very quickly, I thought that it would be bigger for some reason. We didn't see fairies anywhere else in the park, although once we saw Peter Pan being chased by Captain Hook in Fantasyland.
At the Bibbidi Bobbidi Boutique, fairy dust runs through the mirror to light it up, that was a neat fairy touch.