Note: This article pertains to Mac OS X Server versions 1.x, which were released prior to May 2001.
In this case, MacOS.app is a wrapper. A wrapper is a directory that contains an executable and any resources the executable may need to operate. Wrappers contain the kind information that would be stored in the resource fork of a Mac OS 8 application, such as icons. Resource forks can not be used with Mac OS X Server because the UFS directory structure does not support forked files.
The Workspace Manager makes directories ending in .app, .pkg, or .mpkg wrappers and thus double clickable. The command line does not have this functionality which is why this difference is noticeable.
Wrappers can be opened by holding down the Command+Shift+O keys, or by holding down Command+2 and pressing the Open Application Wrapper button.
Older command line utilities like the ones in /bin and /sbin do not have a wrapper because they do not have a graphical interface, and therefore must be executed at the command line.