Modification best practices

In the video tutorial on using template hooks, I believe I understood from Kier's explanation that using template hooks is preferred to hard coding templates themselves due to potential for out of date templates causing upgrade issues.

There are tons of template modification suggestions all through this forum, so question is how much of an impact are code changes in templates, or did I misinterpret the template mods vs upgrade issue.

At this point I am adding my own template hooks in several places, and instead of modifying existing template I'm creating my own version of it and replacing original with a listener.