You could try my ioq3 new filesystem project. It's an ioquake3 modification specifically designed to support more pk3 files. It can handle all the pk3s on lvlworld at once, and a lot more.
I did post on the ioquake3 forums a while back. I haven't heard from any of the main ioquake3 developers, though.
Hello. I've been working on an ioquake3 modification that I think may be useful to custom map fans. It uses a new system for loading pk3 files, which can support thousands of pk3 files in baseq3 simultaneously with minimal resource conflicts or load time impact. It has other improvements too, like more reliable download support and debugging commands for map developers.
You can check out the project here:
Windows test builds:
Note that this is currently just an engine modification, so it doesn't by itself change limits on how many maps will show up in the ingame menus. That depends on the UI code from whatever mod you are running. If maps don't show up in the menus you can always use the /map command to run them.
I'd love to hear any feedback!