I have a mix of both have not experience any issues.
I have NAS based on freeNas - had it before linuxMCE - which I use to backup linuxmce video and audio to; it is not setup in linuxmce - that is - I choosed ignore. On my production core, I had a 750 G drive, just for media, which I let linuxmce configure; planning on when I properly recreate the production system, to simple remap the original /home/public/data/ directory to that of the new media disk (have to create all folders as in original directory), so all media go to the other drive, the original just for binaries and diskless images; plan on using an adaptec card 4 port, raid 0, three disk, as I will be backing up to the NAS.
You can use a raid card to handle the drives, or your onboard raid if you have the appropriate driver support, or linuxmce built in raid.
Personally I like the raid card option as the ones I have used support hot swapping, thus in combination with a hot swappable case, a drive fails, you simple pull it out and put in a new one, less steps than software.
Drives internal saves you power as you do not have the additional electronics to power continuously.
See the links below:
http://wiki.linuxmce.org/index.php/Create_RAID_in_LMCEhttp://wiki.linuxmce.org/index.php/Create_RAID_in_LMCE_ManuallyThis is also the link for the wiki, lots of other stuff
http://wiki.linuxmce.org/index.php/Main_Page