But a majority of Manhattan crosstowns in particular did NOT have the current #ing system & were renumbered in the 1980's to have numbers correspond to the street name. Lets see if I could remember off the top of my head:
M22--same but modified
M21--same but modified
M13--now M8
M14--same
M26--now M23
M16--split to create M34
M106--now M42
M27--split to create M50
M28--now M57
M29--now M66
M30--split to create M72
M17--now M79
M18--now M86
M19--split to create M96, M19 renumbered to M106 in 1995
M20--now M116
For Queens, the 50's [54,55,56,58,59] were numbered that way to identify them as Brooklyn-Queens routes and the 70's [74,75,76,77,79] are identified as routes that don't run 7 days a week.
For Staten Island, Kool-D explained the structure for the routes when they were renumbered in the late 1980's [and still have the same structure to this day].
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As you said, there is no unique numbering system in Brooklyn, most of Queens and the Bronx.