No. It's not related. It's also not really a problem. updatedb completed successfully, but couldn't read that one location and let you know about it.
updatedb crawls every file on every filesystem mounted somewhere on /. However, /run/user/1000/gvfs is a special mountpoint used for the gvfs FUSE filesystem. It is explicitly set up so that only you, the user with UID 1000 can access it. Not even root has access to it. When you are running sudo updatedb you are elevated to UID 0 and no longer allowed access to /run/user/1000/gvfs, so it prints out that error.