I think this depends on what size of files you are talking about. There are some important considerations when implementing a BizTalk FTP architecture. The following article mentions these: http://technet.microsoft.com/en-us/library/aa561801.aspx. The main suggestion is to implement multiple handlers under a single host rather than simultaneously running hosts so that there is no overlap in the files processed through BizTalk.
I think this is a fine approach for small files. You should also look at the distributed file system technology: http://www.microsoft.com/windowsserver2003/technologies/storage/dfs/default.mspx. You may need to implement some custom logic to pull the files from FTP but this would be a simpler file management solution.
Thanks,