There is a tacit push for weeding out old dependencies as older scripts are restyled or improved by adding the new Header class or bumping up the dependencies version. I strongly recommend that if a dependency is changed, a comment be placed at that point in code indicating the change. Also note that we seem to be seeing several issues lately from our more mature code which could be attributed to a dependency change therefore, one might start there when looking at new issues/bugs.
BTW: Concerning those depreciation warnings, guess what? They mean it.