I'm not sure but I think if you delete a route you are only deleting the map.
You are correct. You only delete the route map you selected for deletion, not any of its downloaded dependencies. The same goes for other assets, such as sessions or rolling stock, that reference and download additional assets - e.g. a rolling stock asset that includes bogies, couplers, commodities, etc, the rolling stock asset will be deleted but its bogies, etc will remain.
If some of the items are on third party sites they will show up as unknown objects and give you a missing dependencies error. You can open the map and delete missing dependencies to get rid of the error.
Again correct although the term "Third Party" can be misleading. In Content Manager the term "Third Party" can mean that the asset was originally downloaded from the DLS but has since been withdrawn, permanently in the case of a copyright violation, or temporarily if it is undergoing repairs.
Often, as you point out, the problem of missing assets can be solved by using the
Main Menu Tools option
Delete Missing Assets particularly if those assets are just scenery items which you can easily replace with other assets. However, sometimes those assets are crucial items such as track or track assets in which case their absence can make the route unusable. My general policy is that unless I judge the route to be "worthy" and repairable, then I simply delete it and retain any of its assets that were downloaded from the DLS. I gave up on playing the "Hunt the Missing Assets" game years ago.
My thoughts and experiences
