My experience (which is only four months!) is 'no'.
I downloaded a scene, removed assets I didn't want, saved under a new name (so now stored in my 'VaM/Saves/scene' folder), then remove the original file from VaM (using File Explorer, removing the file from 'VaM/AddonPackages' and storing it out of VaM to test what would happen). I suspect, as Hazmhox indicates, the paths to the assets used in the saved file are still collected from the original var file.
However, if you remove the assets you don't want from the scene, then save the original file, that works. Of course this means the scene is permanently changed on your PC but you can still download the original from the Hub, if that's where it came from. I mostly removed Person atoms but also some objects like chairs.
That's my expereience anyway!
Loading times for scenes with scenery, like classrooms, still takes time though. I just do something else, on my PC or clean the house!