Yes, the guns are checked for stolen (or should be) and out here all guns are sent to the Texas Department of Public Safety Lab to be checked ballistically (sp?). We have several guns that had been in the evidence room for years that are at DPS right now being checked. Once they are cleared, and we get the disposal orders, they will be converted to departmental use, where applicable, or probably traded to a LE retailer for credit towards equipment, or destroyed depending on condition.
If the gun comes back with any type of history, then further checking is done. The shotgun that was used at the federal courthouse in Las Vegas was traced back to either Memphis or Nashville TN Sheriff's Dept. It had been legally sold by the department to a retailer, legally sold by the retailer, and it eventually made it's way into the hands of a loony-toon.
I once had a shotgun that was stolen from me in a residential burglary. It ended up as a murder weapon about 5 miles down the road from me. It was allegedly bought at a flea marked on the other side of town. I know that the Sheriff's Department did some checking into the purchase, but never came up with anything. I spent alot of time at the flea market trying to see if anything else would show up there, but nothing ever did. I had to give a statement and reference the burglary report. My rounds were even used in the murder. The serial number was "drilled" off of the sideplate, but acid was used to bring it back up.