Please try Eeschema Preferences > Hotkeys > Set to Defaults. Some hotkeys were changed to align the tools with Pcbnew and this may cause conflicts. I cannot replicate any of the issues you list:
1) Ctrl+D for duplicate works fine (can hover over or select items), Ctrl+C for copy to clipboard requires the items to be selected.
2) I think this was fixed recently.
Please try Eeschema Preferences > Hotkeys > Set to Defaults. Some hotkeys were changed to align the tools with Pcbnew and this may cause conflicts. I cannot replicate any of the issues you list:
1) Ctrl+D for duplicate works fine (can hover over or select items), Ctrl+C for copy to clipboard requires the items to be selected.
2) I think this was fixed recently.