The number seven definitely bears significance in several Ancient religions and cultures. For the sake of discussion, I will be focusing only on the Islamic significance of the number. As a Pagan, I, myself, believe in the seven chakras of the human body. I do believe
there is divinity associated with the number seven. If I began to write about it, however, it would occupy too many pages.
In the Qur'an, mention of the seven heavenly bodies is NOT referring to the seven layers of the atmosphere. Here are my thoughts about what it could in fact be referring to (Keep in mind that I do believe that some parts of the Qur'an are divinely inspired, clearly demonstrated in its eloquent sentence structure and numerical, as well as scientifical information).
The seven classical planets were: The Sun, Moon, Mercury, Venus, Mars, Jupiter, and Saturn.
These were all visible through the naked eye in ancient times (They had outdoor lifestyles, and were much better at observing the skies than we are, we are in fact too ignorant of that, plus we have "light pollution")
Qur'an 41:12 - "And He completed them as seven heavens within two days and inspired in each heaven its command. And We adorned the nearest heaven with lamps and as protection. That is the determination of the Exalted in Might, the Knowing."
What is "the nearest heaven", according to my interpretation of the word heaven?
Venus is the closest planet to the Earth. Furthermore, after the Sun, it is the brightest of the seven heavenly bodies, too.
Let's do a linguistic analysis (Again, I'm not an Arabic speaker, so I'll be using Google Translate. However, if YOU are an Arabic speaker, please correct me!):
The word used for "heaven" in the Qur'an in 41:12 is samāwātin - heavens (Thanks, Sahih Muslim!)
Let's go to Qur'an 2:255:
"Allah - there is no deity except Him, the Ever-Living, the Sustainer of [all] existence. Neither drowsiness overtakes Him nor sleep. To Him belongs whatever is in the heavens and whatever is on the earth. Who is it that can intercede with Him except by His permission? He knows what is [presently] before them and what will be after them, and they encompass not a thing of His knowledge except for what He wills. His Kursi extends over the heavens and the earth, and their preservation tires Him not. And He is the Most High, the Most Great."
Notice the scripture says "heavens AND the Earth". The "heavens" can not in fact refer to the "skies", but rather, celestial bodies, as the skies are already part of the Earth, so saying "heavens and the Earth" would be redundant.