The reason why the templates are installed every time you update is because they are included in the install package. The install package isn't what you would expect.
If you are updating from (for example) Joomla 2.5.13 to 2.5.24, the zip file that gets extracted doesn't only contain the files that were changed for this specific update. What Joomla does is they have a massive update update zip that contains all the updated file since Joomla 2.5 was first released, and they continue adding modified file to this zip file. Admitedly this can be annoying as it makes the zip file that gets extracted on your server quite big, but it also contains all the previous updates. So in regards to the template, this was updated at some point (not sure which version the changes were made), which is why the templates get re-installed each time.
Joomla 1.5 was different. They created a separate zip file for each update but it made life very hard as you can not be sure which version they are updating from. So rather than creating lots of different zip files, everything was merged into 1.