There is a folder ...\Qlik\Sense\Client\hub\img\core\logo which holds the logo files, the Qlik Sense server logo is called sense-server.png.
I had a quick go and managed to swap out the logo for a custom one, you will need to keep the filename the same and also you will need admin rights to the folder. You should be able to do this with the favicon and other media in these folders too.
Once you've got your custom logo in the folder you should be able to see it in the hub once you refresh, you may also need to disable browser cache to see the change, in Chrome this option is found in developer tools -> settings -> network -> disable cache.
I don't know if Qlik Sense server will try to overwrite these files at some point but doing the above worked for me when I tried just now!