My understanding is NCIC is not reliable, many local agencies don't report stolen guns, if a gun is returned to the legal owner the entry is often not updated, etc. I don't really know or care much about it, but that is what I was told in the past.
I've used this site before to check on questionable guns I've worked on. Most recent was a SCCY that had a broken receiver and came in jammed. It was clear, and the manufacturer replaced the gun with a brand new one.
Its not a bad idea if you are going to work on a public gun to just check to make sure it isn't on a list. Never know if you are working on a "smoking gun" if its not yours.