'All but certain' means he (the inspector) is as close to certain as possible without being completely certain. After all, he is not a doctor and is therefore not qualified to declare somebody dead.
You are getting confused with another structure - 'all + noun + but' - e.g. all the guests but Kevin brought gifts. Here, in this structure, 'but' means except. In your idom, 'all + but + adjective' it does not. Similar sayings are - all but decided, all but finished, all but won. All mean as close to this adjective as is possible without being completely there.