I can't see how any airline needs more than 3 digits to identify the flight. ... And eliminating '7' from those three digits still leaves 900 flight numbers available.
Btw, I haven't heard any flights called 'XX' 000 either, which I assume must be intentional.
Traditionally, airlines do not offer a flight #0. Many times flight #1 is the first numerical flight number, but not always, depending on the airline's naming conventions of their flight number sequence.
But to your first point, most major airlines offer more than 1000 marketing flights. And most legacy carriers with regional feeders organize their flight number naming conventions. I'll use Delta Airlines as an example (this is not current, but is an example of a few years ago):
1-190 International flights
200-1800 Scheduled domestic flights
1801-1999 Skywest flights
2000-2800 Song flights
3000s Skywest flights
4000s ASA flights
5000s Comair flights
6000-6199 Freedom flights
6200-6399 Chautauqua flights
6400s Shuttle America flights
7000s-8000s Code share flights
9000s Charters, Ferry flights, stub flights, etc.
This is not currently Delta's flight # breakdown due to the merger (incorporating Compass, Mesaba, and Pinnacle flights).