Efficiently using multiple docker containers in a single host
Since all process run on the native host (you can run ps aux on host outside container and see them). There should be very little overhead. The network bridging and IP Tables entries to forward packets to virtual host will add some CPU overhead but I can't imagine that being too onerous.
If the question is several nginx + 1 mysql versus several containers with each nginx + mysql, probably performance wise would be better not using containers, mainly because mysql and how much memory can have if is a single instance vs having multiple separate instances. You can anyway have the nginx in separate containers but using one central mysql for all sites, in a container or not.