I had a 1TB RAID5 array and Windows is showing "corrupt $Mft" and "unable to read file" errors. It says I should run chkdsk but I've heard not to do that when using RAID.
Whether or not the underlying physical storage device us using RAID has nothing to do with checking the integrity of the filesystem with tools like CHKDSK, fsck, etc.
The only way to check filesystem integrity is with a tool like CHKDSK, anyway. If you have "corruption" you're going to have to use such a tool.
How's your backup of that RAID volume, anyway? Sounds like you might be getting to put that backup to good use.