Mono.GetOptions is deprecated because its author has disappeared from the face of the earth and no one has volunteered for future service. This is not true.
NDesk.Options / Mono.Options are "unstable" in the sense that the API is essentially unstable - I reserve the right to change the public API in an incompatible way if I consider it appropriate. (I hope I don’t need this, but I leave it right.) However, I am still there, so it is supported (or can be supported).
This is why Mono.Options is distributed as a source - if the API changes, it does not matter, since you have a copy of the source associated with your program. (Also, why NDesk.Options.dll is not signed - therefore, it will not be placed in the GAC, since assemblies in the GAC have a strong assumption that they will not change the API in an incompatible way.)