Nothing to worry about regarding the three packages it just means their not checked into your master repository. They're not required for VSE to run correctly.
I'd be more worried about the fact that you're not running the lastest patch for 8.8, which is currently Patch 4.
Agreeing with Tristan here. Nothing to worry about here unless you are in fact trying to get the superdat, extradat, etc... Those directories on your distributed repository will only have new data for the endpoint to download if you are pushing out a Superdat, extradat, etc... from ePO. You'd usually do this on a given day in response to a zero day threat or vulnerability patch. If your daily DAT/Signatures fail you will see a much more clear message saying something along the lines, "Update Failed". As for verification, here's a page you can always go to to compare your DAT with what the latest is: ftp://ftp.nai.com/commonupdater/