"Our Father who art in heaven . " is probably the most well known saying of Jesus in the Bible. This saying or prayer is not recorded in 'Thomas', yet the word Father appears more than 20 times. So Jesus obviously considered Father to be an important word that held a strong meaning to his listeners.
Jesus uses Father to describe aspects of the Kingdom (another common word in 'Thomas'):
The Kingdom of the Father is like a man . [Logia 57,76,98]
The Kingdom of the Father is like a woman .. [Logia 96,97]
As well as in the more normal sense of parent or guardian:
That one is your Father [#15]
You will not see the Father [#27]
He who blasphemes against the Father [#44]
"What is the sign of your Father in you?" [#50]
At the time of Jesus, fathers had a strong and important role in the family. A father was expected to provide food and material goods, to guard and protect, to have authority, and to instruct and lead their sons. In fact in that society the son was generally the apprentice to the father; "following in the father's footsteps". Sons without fathers would find it hard to earn a living, and fathers without sons would lack security in old age. It's no wonder that fathers Joseph and Zebedee may have been dismayed at their sons' new directions in life.
These qualities of the 'perfect ' father are the key to Jesus' use of 'Father'. They are aspects of our Real Self that we can not only draw upon during our spiritual journey, but also will manifest themselves in that very special relationship between parent and child and other relationships.
So why is "Our Father who art in heaven . " missing from 'Thomas'? That phrase is the quintessence of the duality of God and Man. It would lead us away from Jesus' message on Oneness that lies at the core of the Gospel of Thomas.