The northern reefs (Barracuda, San Juan, etc.) are not closed. We just dove it two days ago. However, permission from the harbor master is required the day prior to the planned dive. The dive op must present a written request including the names and levels of all divers as well as copies of each divers c-card. This has always been the requirement, some shops simply won't bother with it or cannot get permission due to previous incidents or lack of experience of the divers.
It is considered expert diving, so we don't take just any diver up there. This is why permission is required because the currents are very fast and topside conditions are rough. If the group gets separated (which does happen up there) it is very difficult for the boat to see you, especially without a signal buoy. The next stop is literally Cuba, so getting "lost at sea" is a very real possibility up there without the right crew and experience among the group.
As far as best sites to see Eagle Rays, it is up at the northern sites in Dec - Feb/March, they can be seen at any site, you just never know. Thye are fairly seasonal and we rarely see them in the summer months when the water warms up.
Hope this helps.
