It doesn't make a difference for organizational purposes, S3 folders are really just an illusion for the benefit of humans like us so that it seems familiar - there really are no physically separate folders like there are on your own machine.
The naming convention you use however will have a tremendous impact on performance, once you get to a certain point (for small number of files, its probably not going to be noticeable).
In general, you want the beginning part of your file/folder names to be 'random-ish', the more random the better...so that s3 can disperse the workload better. If the name prefixes are all the same, there will be a potential bottleneck. A short random hash at the beginning of each filename would be probably give you the best performance.
Right from the horses (AWS) mouth:
The sequence pattern in the key names introduces a performance problem. To understand the issue, let’s look at how Amazon S3 stores key names.
Amazon S3 maintains an index of object key names in each AWS region. Object keys are stored lexicographically across multiple partitions in the index. That is, Amazon S3 stores key names in alphabetical order. The key name dictates which partition the key is stored in. Using a sequential prefix, such as timestamp or an alphabetical sequence, increases the likelihood that Amazon S3 will target a specific partition for a large number of your keys, overwhelming the I/O capacity of the partition. If you introduce some randomness in your key name prefixes, the key names, and therefore the I/O load, will be distributed across more than one partition.
If you anticipate that your workload will consistently exceed 100 requests per second, you should avoid sequential key names. If you must use sequential numbers or date and time patterns in key names, add a random prefix to the key name. The randomness of the prefix more evenly distributes key names across multiple index partitions. Examples of introducing randomness are provided later in this topic.
http://docs.aws.amazon.com/AmazonS3/latest/dev/request-rate-perf-considerations.html