Sounds as if you want to use the archive to group your files.
From a reading the files point of view, it makes very little difference if the files are handled one way or the other. You would need to implement the ability to read zip files, though. Even if you use a lib like James Curran suggested, it means additional work, which can mean additional sources of error.
From the uploading the files point of view, it makes more sense: The uploader could gather all the files needed and would have to take care of only one single upload. This reduces overhead as well as error handling (if one uplaod fails, do you have to delete all files of this group already uploaded?).
As for the efficiency of reading them from the archive vs. reading them directly from the disc: The difference should be minimal. You (or your zip library) need to once parse the zip directory structure, which is pretty straight forward. The rest is reading part of a file into memory vs. reading a file into memory.