BA have had 4 digit flight numbers for years. From memory in the early '80s:
0-299 Long Haul
300-999 Short haul (excluding domestic UK)
1000=1299 extra long haul,
1300-1999 extra short haul
2000-2299 Long haul Gatwick
2300-2999 short haul Gatwick.
I think domestic German (Berlin) were 3xxx, non London domestic 4xxx
With the advent of code shares 4 digit numbers have mushrromed (and made a bit of a mess of the BA system of numbering). It is said that Delta ran out of 4 digit numbers over 10 years ago. They asked IATA for a 2nd two character code but they were refused. If you look at some of their domestic flights you will find A-B-A with the same flight number.
In such circumstances not using 666 or 13 or some other numbers may not be practical.
A question is whether 0001 is diferent to 1. I doubt it but does anyone know.