What exactly do you mean with original? There is no such thing as original in the context you provided. Downloaded digital files are always copies.
If you fear data degradation, archives are lossless compression, as hechelion explained. Image compresssion as with jpgeg files is lossy, there is a difference between stored and displayed and when your recompress.
All that being said, there can be some technical differences. Meta data in the archive and even the file name of the archive. And of course if you keep the files somehwere, where they might be modified. For instance if the rom comes with a save game or whatever. It is bad practicse to modify installed files, but we are talking about homebrew roms here and I have no idea what is done there.
If the archive was merely a way of transporting the files and the files were not modified, you can just rezip them to have a new archive for safekeeping somehwere not so tiny as a thumbnail.