I might be able to dig an application that can pull this off (I have none to hand) but can I instead suggest you rethink your method:
If it is zip then it is straight up file compression on a file by file basis whereas stuff like 7zip tends to use data hence it working so well for big collections of roms (note that using 7zip in this manner will probably make extraction even longer).
If you must zip them then perhaps a lower setting is in order, as someone who has done compression algorithms from the ground up in general computing most of the compression gains are achieved with the simplest of methods or weakest of settings (case in point; ever noticed how a trimmed DS rom and a plain zip compressed rom are about the same size or if you go in for the PSP as your signature implies how a basic level of CSO is not that far off a level 9 in terms of percentage gained).
I will flip it again; you say 1000 odd files, I am guessing some are of the "potential to be used" rather than "every day", how about shifting them to a secondary archive.
Similarly if you have 1000 files in a folder you have probably messed up somewhere or could stand to sort them better. The time to do this is now (or ideally a few months back but as my time machine is reserved for more important things like looking at dinosaurs that is not going to happen) before it becomes truly entrenched.
The next is what sorts of files are they; if they are all documents or all images or all something else we might have different options including no compression for formats with compression already inbuilt (most image formats, music formats, video formats and a good chunk of document formats).
Rather than straight up compression how about diff files or something like it, for instance xdelta is built for this (although we usually use it in these circles for distributing rom hacks).
Next there are all manner of compressed file systems ranging from compressed mountable ram drives to actual set in magnetism tracks. By similar token how about a new partition of the drive you are using or even a new drive for the files in question.