I just added a comment to the issue, but wanted to get your thoughts on this: What if we simply output a warning for now when we discover a case where we think you might need to update your script references?
Most web developers will have their script references centralized (for example, using layouts etc) so ideally there's only one place to update the scripts. So updating the scripts is not the painful part. The painful part is knowing which ones need updating.
So we could play it safe and simply issue a warning. There's a couple of heuristics we could try:
If the new package contains a js script (or css file) that's new or non-existent in the previous installed version of the package, output a warning. If this is the first time this package is installed, output a warning for each script/css file.
Same rules as the Simple case, but scan the project for places where the script/css file is referenced and output a warning with specific information.