You can change that. Create a unique folder on your computer and put the logo in it. When you create a new presentation or when you create a template use Insert and link instead of just linking the logo.
Click Insert - Picture - navigate to the special folder - select the picture - then click on the downward pointing triangle next to it. Choose Insert and link from the dropdown menu that appears.
Now if you replace the logo in the folder (using the same filename) PPT will automatically update the file when you open it.
If you delete or move the logo to another folder PPT will use the most recent embedded version. This is only the case if you choose Insert and link and not link. When you use the latter and move or delete the picture you will get an empty placeholder with an x.
