IMO, canon is pretty clear that all primary Federation civil and diplomatic functions are carried out by Starfleet's NCC vessels (which is IMO consistent with IRL), other prefixes do exist.
ECS - formerly Earth Cargo Service, may still be in use for UE flagged civilian vessels (cf the Xhosa).
NAR - appears to designate civilian surveyor and colonial support vessels.
NBT - no information, the 'T' suggests a transport ship.
NFT - transport ship, only appearance was a private (?) character by El Aurian refugees.
NGA - civilian transport ship
NSP - apparently 'Vulcan National Merchant Fleet', likely (lightly armed?), mostly for cargo but can act as a small troop transport in extremis (likely the Vulcan equivalent of the ECS). May also have been used in a 'Coast Guard' type role (the most common RW uses of SP are either 'Shore Patrol' or the USN WWI era 'Section Patrol' designation for conscripted pleasure craft, yachts and similar).