I doubt you'll find a hard limit. It's more that under most operating systems, the more files you have in a folder, the slower the OS is in doing operations in/on that folder. At least under OSX, I don't think you'd see much native degradation w/ 1000 (maybe 2000 or more) per folder (total guess here). After that, viewing via Finder etc might be slow and cumbersome for you to say 'gee, I should have arranged things differently'.
It's generally faster for an OS to dive deeper than it is to survey a huge flat space.
RE: #2, I would think that is personal workflow preference for file organization.