Off the top of my head:
Nobody questions why main drive is C:, remnant of [an] early computer having two floppy (not sure) drives on A: and B:
Or more recent - C:/Windows/System32 holds 64 bit executables; 32 bit exectuables live in C:/Windows/SysWOW64
It's the Windows way to abstract system folders and provide binary compatibility across architectures. I'd much rather have ld.so.preload and multiarch than this hard links mess though.