'D' is for Destroyer, it's a code Masao Okazaki used cuz there isn't really much space in between the Constitution class registries (his ones run 1700 to 1749, no irregularities) and the Miranda class registries (USS Miranda is 1833), the Avenger and Predator run after the Connie but before the TMP period so this saves the whole question of accomodating the registries. Though it does raise the question of why other Starfleet Museum ships don't follow this scheme, like the carriers could use NCC-V*** or the scouts could have used NCC-S***
Though Mariner really should have used 'F' in this case as the Burke is a frigate. NCC-F301, hmm.
Oh and I don't really like that secondary hull, it's way too spindly when you compare it to the saucer and nacelles of the Burke which are very voluminous.