How can I ensure that updates to restrictions made in Zeevou, such as minimum stay, are automatically reflected in all rate plans on Booking.com, including the related (derived) ones?

You need to contact the BDC support team to activate the 'Enable to follow ALL the RESTRICTIONS from the parent rate plan' option for all derived rate plans.

Alternatively, you can create the same rate plan setup on both Zeevou and BDC, and map each of them one-to-one. More details can be found here.