It's very unlikely Rockbox physically damaged your hard drive - I'm not aware of any cases of that happening in Rockbox's five year history.
But ipods do break (with or without Rockbox), so yes, it's possible you have a hardware problem.
However, the most common reason for filesystem corruption will be to not safely disconnect your ipod from your computer after copying files to it. How you do this depends on your operating system, but if you simply pull the plug then that's most likely the cause.
Let the scan disk finish, and then see what happens.