I am starting a new campaign and a player of mine is playing a Navigator. We were wondering if there was any restriction for a Navigator wearing fully inclosed helms say from storm trooper armor or power armor should that become available in the future. Will he be unable to make use of the eye powers if his head is enclosed and foes cannot see the eye?

Only if the power requires they see the eye. Otherwise I would say no, since the navigator is looking into another dimension.

Or have your local friendly tech-priest customize the helm to include a third eye-visor, so it can be opened without taking the helm off.