E-smith uses the SAMBA file sharing package. SAMBA basicly makes the E-smith server "look" like a Windows machine that has file sharing. With the way SAMBA and file sharing works, there are browse rights and permissions when browseing via the network neighborhood. Meaning you are not allowed to see those other folders.
When you FTP, there are isn't any restrictions on what you can "see", however, I think you will find that if you try to access one of the folders you "see" when FTPing, you will find your access very limited, if at all.
Another way to put it is the other folders you see when FTPing, are simply not being "shared" on the network.
I hope this helps.