Yes ..... Waypoint sharing will not be affected by the mapping card.
The waypoints exist in the units memory, not on the mapping card. The waypoints are just "overlaid" on the mapping image from the map card.
If you are viewing a waypoint on one mapping card .... remove it from the unit and insert the other mapping card, the waypoint will show up on the other mapping card ......Mapping and waypoint / GPS data are independent things.