like I said, the DYRL (and SDF:M) numbers try to mimic US carrier aviation numbers, but are more like US airforce numbers.
lowest number in the navy is 000, which is for an Admirals transport plane. CAG planes end in 00, and squadron leaders end in 01. the first number indicates squadron and aircraft type (1 and 2 are fighters, 2 and 4 are light attack aircraft, 5 is heavy attack aircraft and I forget what 6 and 7 are).
In Macross the numbers seem kind of arbitrary, I want to say that they function like Air Force tail codes where they are the last 3 numbers of the planes serial number, but I have no way to prove/show that.