I think the 16-bit command.com is still there because there are a few differences between how command.com and cmd.exe process batch files and there are probably some companies that still use batch files that may rely on that behavior. If there's not reason (for example, security issues or that the system won't support the program - like Win64), then there's really no reason for MS to remove the program.
And for what it's worth, here's my recollection of the level of support of MS-DOS in the various versions of Windows:
- the Win9x series didn't so much run on top of DOS as used it as a boot loader - once the Windows VMM took over, DOS was pretty much out of the picture unless you had a DOS device driver the system depended on, in which case the VMM would still make calls to it. But by 1998 that was a pretty rare situation (and I think that WinME might have stopped supporting that option). Running a DOS box did run an actual copy of MS-DOS in a virtual machine.
- the WinNT series (including WinXP and later) didn't incorporate an actual MS-DOS system, and it relied on it's own boot loader instead of DOS. However, the MS-DOS compatibility support provided by WinNT was built from source code taken from MS-DOS (version 3.3, I think), so the level of compatibility was pretty high. I'm not sure if code from MS-DOS 5 and later was pulled into the NT supporting code. If my memory serves, most of what was added to MS-DOS 5 and later was support for various disk compression and memory management schemes that wasn't necessary for the NT VM anyway.