In the Netherlands civil registry was introduced in 1811 and from then on surnames became mandatory by law. So all LNABs for post-1810 births must be set to the surname recorded in the birth certificates in the civil registers. Any post-1810 baptism data (hardly available anyway) is to be considered unfit for LNAB use.
Pre-1811 we rely on baptism records, using the surname if present, or else the father's first name (patronymic).
This of course raises the question of which method to use for migrating ancestors. I seem to remember that initially the New Netherland Settlers project used the "Dutch" method, but some time ago switched to the one described above by Ellen, making it harder for the Dutch to find pre-migrating generations...