It was really a single system in 1971 that kicked off this trend. Originally /usr was for user files, like /home is today (do you'd have /usr/dmr, /usr/ken, etc.) / and /usr were two physical disks, and at some point the / disk (a 1 or 2MB disk IIRC) was full to they put some things from /bin in /usr/bin as a hack. And it's "stuck" since then. This is why /usr has such a weird name, because it was intended for user files (/system, /software, /additional or something would make more sense, abbreviated to /sys, /sw, or /add of course). Initially Unix was a quickly developing system for internal use, but it was actually used and there was often some tension between "do the right thing" vs. "don't break too much". Some of the weird things in C are due to that as well (e.g. &'s precedence being a good example).
I guess some other systems that ran Unix ran in to similar problems, but by the time unix started to gain some adoption in the mid to late 70s disks were larger too, so I don't know if it was ever really needed beyond that initial research unix system used only internally at Bell Labs. I believe they updated the disks on the original Unix system not too long after this making this hack superfluous, but they kept it for compatibility (and because it might be useful again in the future).