I’m not sure that i understand very well because i’m not so far familiar with english, so, don’t hesitate to tell me if it’s something else that you search. There’s an option to remove the logo:
yunohost settings set ssowat.panel_overlay.enabled -v False
If you only want to remove on an app and not everywhere, you must use a hook like in this post:
I don’t understand what you mean. If you modify a file, you can’t use the webadmin? I don’t think it’s the case, i’ve never seen it. Could you please elaborate?