I just tested this in the 5.0.0 release and was able to change the kibana.svg logo file and see the results in Kibana. Here's what I did;
I used InkScape to edit src/ui/public/images/kibana.svg and saved it.
I copied that modified file to optimize/bundles/src/ui/public/images on top of the kibana.svg that was there.
I refresh my browser and saw the modified image.
Then, just to be sure, I stopped Kibana, started Kibana, refreshed my browser, and saw the modified image.
Then I stopped Kibana again, deleted everything from the optimize directory, started Kibana, waited for Optimizing to finish, refreshed my browser, and saw the modified image.