You can have as many subfolders as you want - there may be a theoretical level as well as a practical level but within reason you should have no problems.
As for backups, again no real problem.
For what it's worth, I have a partition on the disk called my data. Within this is MyDocumnents, my photos and so on, and within my photots are perhaps 8 levels of subfolders (and growing). This is easily backed up to another disk daily.
click here - excellent and free software for viewing your pictures.