Welcome to Trainz.
I find it best not to use the update feature.
Just update assets as you come across them in the routes or assets you are using.
My TS12 has always shown about 2000 and after N3V did a massive update of built-in assets for the new version coming out, it rose to over 10000.
The assets that need to be updated will show up when you list the dependencies in Content Manager, by right clicking on the route or asset and choosing 'view dependencies'.
To update just right click on the item and choose "Asset version' and follow the screens to download the update.
The asset will still usually work without the update.
Cheers,
Mike