Josh Donaldson used to be a catcher, that is definitely in the past and he won't be going back there. But in an emergency due to an injury to a catcher he could finish a game behind the plate. (in an emergency only).
Martin is the catcher, Navarro DH. Navarro could catch 1 in 5 games or so. (maybe catch MB) and Martin could DH that game.
If Martin is being counted on a your #2 hitter, you probably don't want his bat out of the lineup for 20% of the games.
Under this scenario most teams would still feel the need for a 3rd catcher on the roster (IE Thole) in case there is an injury to the starting catcher in game. IE if Navarro is DH and Martin gets hurt, you would need to remove your DH and have your pitcher bat for the rest of the game.
I think the risk of this is low enough that I would take my chances and not carry the 3rd catcher and waste a roster spot.
You probably would not pinch hit for either Martin or Navarro. Martin because he is too good of a hitter to pinch hit for and Navarro is a switch hitter and would not be exposed to certain relievers. You would lose the ability to pinch run for Navarro when he is catching, but you could still pinch run for him when he is the DH (which he would be 70-80% of the time).
The Blue Jays would likely have a 7 man bullpen. Meaning a 4 man bench. It would give you so much more flexibility to not have to waste a roster spot on Thole. You could have a bench of Mayberry, Pillar, Goins, Tolleson or Smoak. A lot would depend on who the 2nd basemen is. If its a average-below average defender you would want Goins around as a potential defensive replacement. If its a lefty hitter with pronounced splits you might want Tolleson as a Platoon partner.
I would probably keep Thole and send him to AAA as insurance in case of an injury or if Martin and Dickey don't click.