In Star Trek the Wrath of Khan, it is revealed that all starships have a prefix number, allowing other ships to order a starfleet vessel to lower its shields. This was created in case a vessel is captured by an enemy.
By the 24th century and beyond, is there any evidence that starfleet vessels still have prefix numbers?
I would think they would be a huge risk vs the borg, and off the top of my head I can remember the episode Message in a Bottle in which the Romulans steal a new federation ship. While trying to retake the ship the other starfleet vessels do not use the prefix number.