Here are a few reasons why I set up my computer in this way:
1) I would eventually run out of room on the smaller SSD if I stored all my pictures/music/etc on it, and for the most part a spinning platter HD is plenty fast. I do keep my LR catalog and previews on the SSD though, for fast access.
2) Putting it on the larger HD in more generalized folder structures (just "pictures", "music", etc folders at the root level of the drive) makes them more available to other applications and users, instead of having them locked away inside the rights-restricted home folder of one user. Even though I am the sole user of my mac, theoretically I could create another user account, and simply tell iTunes/LR/etc on that account to plug in to the music/pictures folder on the main HD, and I'd be good to go. I think in the "traditional" way of doing it, another user would not have access to the docs/pics/music folder of anyone else's home folder.
3) makes backup/disaster recovery easier since I just have to back up those high-level root folders to save all my images/music/etc. Also if I ever need to reinstall my OS or the OS gets corrupted, I can wipe the SSD and still keep all my data structures intact, just need new symlinks to "plug them back in" so to speak.
However, I do enjoy the simplicity/little benefits of having everything located within your home folder, the way "it's supposed to work". For example, the finder has a hard-coded shortcut key to open the documents folder, shift+cmd+O. If you simply made another folder on your HD and used it as your documents folder, you would lose access to this hotkey since it would just keep opening your (unused) "default" documents folder. Using symlinks tricks the OS into thinking that the target folder is in your home folder, but in reality it can be somewhere else. Therefore, you maintain all the special "privileges" that the OS gives to these special folders, but have the freedom to relocate them wherever you want, in order to take advantage of having 2 physical drives. Also, multiple users can have symlinks that point to the same folder (as described above) so you can more easily share data that way.
It's slightly different than moving your entire home directory to a new drive since you would still run into permissions issues with other users trying to get data from another user account folder, also I only wanted specific folders on the data HD, not the entire home folder, since many apps use the home folder for things like scratch disk space, temporary files, etc. that would benefit from the fast access being on the SSD, and also keep the data drive clutter free. Symlinks allows you to segregate the data on a folder-by-folder (perhaps even a file-by-file) basis, while keeping the illusion that it's all in one spot. Personally, I also think the home folder is still subject to "bloat" or "user rot" (accumulation of junk and obsolete files as time goes on) and so there is incentive to keep the actual data separate from the home folder.
It was a bit of an experiment for me when I first set it up, but so far it has worked out pretty well.