The EvernoteHelper app is needed for the following:
1) To allow global shortcut keys to work when Evernote isn't running
2) To have the Elephant icon in the menubar when Evernote isn't running
3) To help the Safari clipper plugin do its work when Evernote isn't running.
That being said, there is currently a bug where if:
All global shortcut keys are disabled, "Show Elephant in Menubar" is unchecked, and the Safari clipper plugin is disabled, the EvernoteHelper app is launched anyway.
We plan to fix this. In the meantime, if it's any comfort, I can assure you that it's not spying on you.