I haven't done this myself. You should be VERY careful with what you do here because if this might end very badly - you'll be unable to access your shares and be left with only the telnet access. So unless you're confident that you can recover from such mistakes I suggest you don't do it.
This change should be reboot persistent. Right?
Unfortunately, no. These files are not located on some persistent storage - they're in a filesystem that's entirely in memory. You'll need to:
1. Create a script in /ffp/start/ containg a similar line of code that adds some configuration to the original.
The content of the script should be something like this:
#!/bin/sh
#Add the following three lines to the [ global ] stanza of /etc/samba/smb.conf:
#domain master = no
#local master = no
#preferred master = no
mv /etc/samba/smb.conf /etc/samba/smb.conf.old
/ffp/bin/sed -e '/\[ global \]/adomain master = no' -e '/\[ global \]/alocal master = no' -e '/\[ global \]/apreferred master = no' /etc/samba/smb.conf.old > /etc/samba/smb.conf
#restart the smb and nmb daemons with the new configuration
smb restart
That script needs more code to stop and then start nmbd and smbd. That's the part I'm the least confident about, since my samba/cifs skills are not that hot.2. Make sure that the script's permissions allow its execution (chmod +x <script-file-name>).
Another thing, once installed ffp the telnet server is always running , right? I'm behind a Firewall (NETGEAR WNR3500) but I don't like the idea to leave some door open.
Is it possibile to shutdown the telnet service or uninstall FFP? Should I simply delete files from Volume 1 
You won't be able to delete ffp completely, because you'll still need it to run that script on every boot. You can, however, disable it from running the telnet daemon. What people ussualy do is follow the instructions to run ssh and after that disable the telnet daemon by removing its execution permissions. See instructions here:
http://wiki.dns323.info/howto:1st_steps