Not that I have noticed after 20+ years of using Trainz. Deletes are always manual (you must do them).
Not sure what you mean by "package items".
Trainz will automatically download updates from the DLS if/when they become available and the original assets will remain installed but with the label "Obsolete" added to their status. You can also update assets yourself using Content Manager. Assets labelled "Obsolete, Installed from Download Station" can be manually deleted using Content Manager.
Assets labelled "Packaged" can be manually updated if a newer version is available on the DLS and the older version will be labelled "Obsolete, Packaged". Ditto for "Built-in" assets. Built-in assets, obsolete or not, cannot be deleted.
DLC assets have be updated, if/when updates are available, from the Trainz Launcher Content Store Updates button. Payware assets can only be deleted from within the Trainz Launcher Content Store Uninstall button, not from Content Manager.
I have been using TRAINZ since the second version came out and assets transferred to later versions. What I wondered was if older versions of assts (built-in,packaged,etc ) were deleted from the hard drive.
Not unless you deleted them yourself, barring a HDD crash of some sort. Transferring assets from an older Trainz version to a newer Trainz version can be problematic, particularly for built-in assets which cannot be transferred over (many of them, if not all, would be built into the new version anyway).
My experience is that I can only delete assets from the DLS or modified. Builtin, packaged and payware items cannot be deleted from CM, although the packages or payware items themselves may be uninstalled, which would remove all the assets involved.