Normally they only change the Interface number for major patches, eg. 5.0 to 5.1, so we should be at 50000 right now. Cataclysm, for example, was 40000 until patch 4.1, and then it became 40100. Someone at Blizzard likely screwed up and typed 50001 somewhere, and since the major version has not changed (we're still in 5.0, not 5.1) nobody has bothered to change it.
Doubtful its a screwup, they used such versions before, for example it was 20003 for the BC release.
Must be some internal reasoning behind those numbers, if they would be always zero why have them?
In any case, i don't think the game even marks your addon as out of date when the last digit doesn't match, however wowace/curseforge are not that smart, they require an exact match. (although i do think 50000 works too for them)