Settings.php is necessary for admin reports but isn't handled automatically like it is for other plugin types. Since admin reports by definition appear in the admin menu (er once you set that up in settings.php) it didn't hugely make sense to have a separate settings page. If you need one it is still possible to add one from there...
(Note: I don't think this is behaviour is 'right', it would be nicer if settings.php worked same in all plugins (e.g. local plugins too) and there was some different mechanism for adding things to random places in the admin tree. But, it's possible to use it to achieve everything you need.)
Agree that the manage page should be present, there is no way to delete them from database (not that this does much harm, but it's sucky).
Note that until various 2.0.x point releases, local plugins and course reports also didn't have any 'standard' appearance on the admin menu. Admin reports have not been singled out for special ignoring. 
So basically, the plugin type is not deprecated.
Petr and others are considering some more standardisation with a new 'admin tool' type which would also be used to reorganise standard admin behaviour [everything else on the admin menu] so that it is less monolithic. So far as I know this isn't finalised or underway, just talked about. If this were ever implemented, I can see it's possible that admin reports would be deprecated in favour of admin tools (because a report is a tool, and is there really a need for two separate plugin types in that case) but this would apply to some theoretical future version - 2.2 or whatever - and clearly not to Moodle 2.1.
--sam