Yes we will still get NSO copies for the future. However, I think the problem with the local registry office is that it is now too late to change this procedure from automatic to fast and we won't have a stamped copy in time for the visa application. The mistake I made was not fast tracking this document shortly after marrying ( I thought she would be applying for the visa Summer 2013 but its been brought forward).
When she visited the main NSO office in Manila (where things can apparently be speeded up) they told her she had to now wait 6 months after the wedding date before such an NSO certificate can be issued.