Raises hand as another pack rat!
I save all my third-party downloads to external drives. This includes all the assets found during scrounging for dependencies and payware content from Jointed Rail or others I've purchased from. I arrange my content by country and then by author. At the present time, this hoard is about 2 GBs of content out of the TBs installed.
I do regular full-backups rather than rely on incremental backups. I've said before that this is a quick and easy way to restore content because it's much easier to find what's there instead of looking through multiple backups. As time goes on, I do purge the older backups since I didn't use them and they took up space. Only once did I need to go back and that was due to a hard disk crash - knocks on wood, walls, and frozen windowpanes for good lasting luck, and will leave cookies out for the LGM tonight.
Over the years, I moved content along from version to version. Eventually, this caused a complete stuff up and crash. The old content really wasn't worth keeping any longer, including old built-in content from old versions.
While we can technically export and save some of this built-in content, the textures are not very good and worse when we've run the assets through Images2TGA. The other issue we run into is old DLC, just like older content, suffers from age just like we do. What looked so great before and worked fine in the olden days isn't quite up to the task anymore. I ran into this not long ago with the Treez Pack from N3V. I installed it because it was available and also due to having some missing dependencies in a very old route. The trees, not even old Speed Trees mind you, had lost their tree shape and were tree branches with mesh blobs where the leaves were supposed to be. If the meshes worked, the textures were broken. I reported this to N3V and they've pulled the product, although I can still download it because I did purchase it and it's in my Content Store.
I do understand your concern when it comes to dependencies. When I restored my January 2004 TRS2004 route, I had nothing missing. What's interesting is when I did that with a version saved from TRS2006, there was some weirdness due to faulty track and switch levers causing white tracks and missing levers. I ended up pulling out what I needed anyway and replaced the white track splines with real ones. In the end, I ended up seriously rebuilding it because it really was horrible!