Plus just cause the highest NCC we saw was 2000 doesn't mean that is the highest number in-universe.
]But the the early ships form Enterpise and what you can see from the daedalus class it seems to go up in a linear fasion.
It's possible that as a ship reaches the end of it's life and is removed from service, that it's number is reassigned to a new ship, and then to another new ship in time after that.
The same way that names are used over and over.
Somewhere in the 24th century, there is a brand new ship with the number 01.