Compress zip files with higher compression

You cannot improve the compression ratio, without decompressing the data. You don't have to extract all of the zip files before compressing them, but I would recommend uncompressing one whole zip file before re-compressing.

It is possible to recompress the files in a zip file one at a time and re-adding them before going to the next file contained in the zip file. This requires N rewrites of the zip file for a zip file containing N files. It is much more efficient to extract the N files and generate the new zipfile in one go, compressing all files with -9.

There is a utility called AdvanceCOMP that does exactly what you're looking for. It recompresses ZIP and GZ files (and some others) without intermediary extraction to disk. (I do believe that the mechanism used is to decompress the data and recompress it, but that does not require writing files to disk or regenerating metadata.)