Is saying, "I am afraid of my father," considered polytheism (shirk) because fear should be directed to God alone? And is "dunun" (nearness/closeness) an attribute of God?

There is no harm in saying: "I am afraid of my father"; for natural fear has no connection to shirk (polytheism). The attributes of Allah are tawqifiyyah (derived solely from revelation), and the attribute of Allah Almighty's proximity to His servants has been mentioned in authentic hadiths. Thus, proximity is one of His active attributes, and He, Glory be to Him, is exalted in His proximity, and there is nothing like unto Him.