If he married and died in Scotland, both certificates should have more details of his parents. Do you have these and do the details match each other and what you already know?
If his mother is Elizabeth Agnew and is noted as married in the 1901 census, then could Johnston have been her maiden name and her son born out of wedlock? If she then married, her son could have taken on the Agnew as he was growing up and then he reverted back to Johnston when older ? Just throwing in some possibilities for you to consider.
You say you know his marriage certificate stated his father was a Samuel Agnew, yet you say he himself married as Johnstone....another possibility that I wonder if you have checked is could his mum have been widowed soon after 1901 and married again, this time a Johnstone, hence him taking on the name? Again, just suggestions to ponder. I wonder that the marriage record did not note him as 'formerly known as' or just 'agnew or johnstone', given that it would no doubt have seemed strange at time that he was usung a different surname from his father.