The real answer is yes and no. MonoDevelop has two different technologies under the hood for reading VS project files. By default, it just looks for certain tags and uses them. This works for project files that are purely generated by Visual Studio.
Visual Studio projects are actually MSBuild files. MSBuild is Microsoft's build engine and has a rich set of capabilities. If you were to customize these files in a way that MonoDevelop does not support in its default settings, you'd run into difficulties. These include creating new types of targets, setting properties in project files, conditional expressions in project files, and so on.
MonoDevelop also has its own version of the MSBuild engine called XBuild, but this is not enabled by default. There is a Preferences setting that allows this to be enabled, but it has been labeled "experimental" for a couple of years now and does not support building MonoTouch and MonoMac projects. This is irksome, since a good build engine is at the core of any complex project.
As it stands, therefore, neither option supports VS project files to the extent that reasonably complex apps require.