Performance Issues & Uploading Documents

Anyone have any insight as to how to improve performance:

1)  using something other than "folders" and "sub-folders" to store documents?  Word is that "folders" are a performance killer.  Question is - what structure works best?

2)  when uploading documents?  Web site indicates each process should be able to upload about 1Gb per hour; realty is closer to 1/1000th of that;

Are folders the cause of the upload performance issue?  Is there any way of improving the upload throughput without running 30 - 50 upload processes?