Hi Marius,
welcome to the forum and thanks for reporting!
The malware scan schedule is a .app Dashboard-only feature. There was a small bug here – if a schedule was set in the Malware Scanner overview, the detail view still showed "off". That’s fixed now – both the overview and the site detail view show the set schedule, and you can change the setting from either place.
For the auto-update settings, the .app Dashboard setting sometimes overwrote the component setting – with version 2.5.3 (releasing today at 6pm), you can change it in both the component and the dashboard, and they should stay in sync (the last switch flipped takes priority).
Feel free to test it out – if anything doesn’t work as expected, please let us know again.
Cheers
Pascal