The trio had been expected to feature in Hadden's set-up following their involvement with Scotland A in the recent Churchill Cup.
But the coach explained that they had not done enough to force their way into the picture for the build-up to the tournament in France this autumn.
While the three were left out, there was joy for five players uncapped at full Test level - centre Calum MacRae, prop Al Dickinson, utility back Nick de Luca, winger Thom Evans and flanker John Barclay.
Hadden said: "There was a great deal of discussion over the selection for every section of the squad, however we did spend longer talking about the back row and the back-three.
"You have to make difficult and tough decisions and in the case of Macfadyen, the main factor behind his omission was that he has not had a lot of opportunities in the season just past.
"He played for the full 80 minutes only three times and that is not enough to show what a player is capable of.
"I have stuck to the adage which suggests that if you are in doubt, you stick with men who are showing consistent form."
On the snub to Beattie, who was in the starting line-up for the final Six Nations match against France in Paris, Hadden continued: "It was always going to be difficult for him to make the side.
"By playing him in all three Churchill Cup games we have him every chance to force our hand - but the fact is that we have four other guys (Simon Taylor, Ally Hogg, David Callam and Kelly Brown) who can play at number eight."
The coach also revealed that Gordon Ross had jumped back in front of Godman in the fly-half pecking order.
He said: "Gordon never loses his awareness of how to control a team.
"It might seem as if I am contradicting what I said earlier in the year, but it was not a problem to me that he did not play a lot in France for Castres in recent months.
"We often need a number 10 who can make decisions on the hoof, and in my experience Gordon is always able to organise a side.