BOOPSI classes go in SYS:Classes, devices go in DEVS:, etc. There has always been this division into directories. They could all be crammed into LIBS: but in the interest of being "clean" and "maintainable" it is probably better not to. The speed penalty is negligible even on a floppy-based system, which is why it has been that way since OS1.0.
Well said. The fact that Amiga did that, instead of just dumping everything in 'system32' or similar is one of the little reasons that all added up made Amiga the best, cleanest, most well designed.