Microsoft programmers have been using system32 since the early windows (32-bit). All the application programmers used this system32 program for their applications.
When windows is upgraded to 64-bit, these old applications still look for system32 folder in windows folder. Hence for application compatibility sake, Microsoft has kept the system32 folder for 64-bit portion of windows.
For 32-bit applications compatibility in windows 64 bit, windows implements WOW (windows on windows) technology, Hence the name sysWOW64 for 32 bit system folder. Even though the system folder for 32-bit programs is sysWOW64 in reality, this folder's name is mapped as system32 to those processes with the real 64-bit system32 hidden.
The windows folder also has a system folder for 16-bit applications. As Windows 64-bit does not support 16 bit code, this folder is empty.
Command.com was a 16 bit program, and as most of the people are used to it, it was left as it is, but in reality it is a 32 bit command interpreter like CMD.exe.
Some quirks of virtual programming at Microsoft.