Sure, but that topic didn’t just store logos. All of the icons and logos specified during setup go here, a lot of communities use the topic exactly as it’s titled, for every asset related to the design of their site.
Even if you don’t change your logo, you still need somewhere to store assets that don’t have a UI option, including for theme components and backgrounds. As an example the banner themes component uses an imgur link for the demo image, if you wanted to use anything else then the Assets topic was the go-to place to store it.
I agree that the topic approach was far from ideal, I remember raising an eyebrow when I first discovered it myself, but now that it has become an accepted practice to store design assets it seems a tad shortsighted to remove it wholesale when the substitute doesn’t provide functional parity.