Good question! The executable seems to be missing in OS X 10.8.x although the man
page for it is still there. Of three 10.8 systems I've looked at, an older executable exists on one in /usr/bin
but it is not known to be part of any installation package by pkgutil
so I'm guessing it was left over from an upgrade from an earlier OS X. A 10.7.5 system also does not have the executable but has the man page. A 10.6.8 system does have it installed:
$ pkgutil --file-info /usr/bin/mdcheckschema
volume: /
path: /usr/bin/mdcheckschema
pkgid: com.apple.pkg.DeveloperToolsCLILeo
pkg-version: 1.0.0.9000000000.1.1248867338
install-time: 1328064907
uid: 0
gid: 0
mode: 755
So it appears that it was at one time packaged as part of the Xcode Command Line Tools component ("Leo" would indicate OS X 10.5 Leopard). I guess you'll have to ask Apple what has happened to it. It could be just an oversight.