Does AES CTR mode store header information in encrypted files?
I would like to ask if that is true for every AES CTR mode implementation?, 


Doesn't have to be. You can store the nonce anywhere. You could even send it to the recipient via a different channel (e.g., email the ciphertext and use SMS to transmit the nonce). Storing it at the beginning has its advantages. For example, if streaming the data, you can begin decrypting immediately.


  and If we want to decrypt a certain block from the middle, we first have to extract the nonce from the first 8bytes and block count in the second 8 bytes ?


Yes, if you want to decrypt a particular block in the middle, you must extract the nonce first, and figure out what the proper counter value should be. Then you can decrypt.