The only problem I'd be concerned about is the life of the CF card. Flash memory can only perform so many "rewrite" cycles in its lifetime before it begins to fail, considerably much less than a regular laptop hard drive. I don't see this as being a huge issue with Amiga systems as they don't allocate virtual memory and temp files to hard drives like the Windows operating systems do, but it's still something to keep in mind if you are doing extensive rewrite operations to the card.
:-D
