I just updated Emesene to version 2 on my Linux Mint installation and I noticed that the tray icon was gone. To bring it back, I did these steps:

1. Start Emesene.
2. In the main window, press Options, which you find in the top bar. Then select Preferences.
3. Click on the Extensions tab in the new window that has opened.
4. There, select tray icon from the Categories drop-down list.
5. And finally select Tray Icon from the Selected drop-down list, which is right beneath Categories.
6. Press Redraw main screen to apply the changes. This button can you find on the same window.