Hypothesis :

I play the plot card 'At the gates' which when revealed allows me to search for a maester character of printed cost 3 or lower and put into play.

Could i search for the character who is a maester as well as a shadow card and bypass the the shadow mechanic/cost and put straight into play ?

Yes. The rules against playing Shadow cards directly does not apply to effects that put cards directly into play.

Just remember that the "s" in the Shadow cost counts as 2 when determining the cost.