Sorry for bumping an old thread, but since this was among the few Google hits for whether Enterprise reservations made through Costco credit properly to National, I just thought I'd add a data point:

When I booked an Enterprise reservation through Costco and put my Emerald Club number in the Enterprise Plus number field on Costco's website, the reservation immediately showed up in my Emerald Club account on National's website, so it appears that it does properly parse Emerald Club numbers as such on Enterprise reservations now.