For fast retrieval you should play around with Folder structure, let it be any OS Windows, Linux etc, when searching happens it checks all file list.
So what you can do is you can have folder structure like 2012 -> 12 -> 20 2012 - year 12 - Month 20 - day
This will help in retrieval fast and also if you can perform indexing it would be great.
Linux or any OS they don't put limit on number of files in folder.