But then the games which are patched but running on a crack should be a-ok or at least close enough to it. Tl dr it would be too annoying and not provide a consistent and acceptable user experience. Users either gave up or posted bug reports that were due to not following instructions to the line. Case and point, the old Mac distribution packages. Releasing the NAM as a simple archive with instructions is a really, really, really bad idea. Again, keeping junk reports out and saving user grief. Due to the complexity and size of the NAM, those tend to turn into issues and bugs. Many cracks out there cause subtle differences in game behavior. I do believe one of the patches that the NAM installer applies doesn't work if the executable has been modified (which changes certain addresses, etc). By discouraging the use of cracked installs, the user doesn't have to deal with these and also keeps users from posting bug/issues that are not caused by the NAM. Many features (including many draggable intersections) will break or not behave properly and sometimes can cause the game to crash.

The game MUST be patched to the latest update (which, depending on the crack, may or may not be the case) for NAM to work properly.

While you do have a point, they have better reasons than just moral grounds: