Because this is the way themes works and the way hugo is organized.
Putting a “theme” in a “themes” folder seems quite a good idea at the time I guess.
Like putting “data” in “data” folder or “css” in “css” folder.
If I follow your question, not why not put all the file on the same root level ? Should be easier ??
And one (of the numerous) brilliant ideas behing hugo is the lookup order. You can override whatever you want easily without changing an original theme and he can be updated on his own cycle.
If you want update the theme directly this is also possible. Going in one subfolder or an other makes no difference at all.