The goal will be always to minimize the amount of folders and give you the ability of balance the distribution. This implementation means 10.000 folders which in fac is more than the ext3 system supports (3200) but that can be tricked (and is tricked) on mostly webservers and by the way they mostly use ext4 (the limit there is 4 billion).
Second thing, the image name will never be related to the id, time or anything because in 2.1 you will be able to change the filename meaning that we can't rely on the filename. This also means that the rw that tonemapped suggest can't be done.We will need either a php redirect or move that folder to something like "oldfolder" and do the rw over the /folder/image.ext --> /oldfolder/image.ext
Now, something that I haven't told you is that Chevereto will support multiple storage structures like multiserver, cdn, the balanced storage and why not the datefolder alternative. There will be a table that will store the storage rules and in the images table we just tell it what kind of storage have this current image. That's why there is no need to relate the filepath either with the real id and the encrypted id, the system, will have this options and I have that in mind that is why I have come up with this system.
I haven't make my mind on what should be the better alternative between /id%/%id/ and /datefolder/ method. For instance, date folders means easy way to browse the real folders and it won't mean a huge number of folders because this means 365 folders each year (27 years to get 10,000 folders) and if you want to balance, just assign each month to a different server or something like that, based on population (is most likely that no one here will set up 300 servers to do the balance in the /id%/%id/ alternative and if you want to balance you go for cdn and things that are way more easy to setup and maintain.
As I said it before, I'm observing all the alternatives.