I don't quite agree with that (Konami), delisting older versions of games that are cheaper and are able to run on lower end systems is erasure and goes against GOG's preservation motto. An option should always be available for everyone.
Plus this version ends up being superior in the sense that it has the copyrighted material intact which will be cut in the new release. The HD version also brings along it's own set of bugs but that's a different story.
Yeah, but is it worth wasting resources fixing an old release just so that they can sell it again on GOG? Maybe, but this is Konami. Either way, the HD versions are superior and the new release apparently fixes some bugs those had. We have to wait for reviews to find out.
What I hope is that MGS1 doesn´t get delisted from GOG because that one is a native PC release unlike the Master Collection version which seems to be the PS1 version emulated. While I understand the PC release was inferior in comparison, it at least looks much better running at higher resolutions and the fan patch fixes most of its issues.