Would agree there is some sense in leaving the hero and shaman in town, but if you are not shielded someone bigger is still likely to hit you  when attacking dead towns,as you described. If you are shielded then there's no benefit  in leaving them in town as you will harvest faster when these are with you, especially if specifically geared.

Makes sense to have Hero and Shaman geared to your troop type, but are you talking about whilst they are in town or attacking?

Pretty sure you only get the bonuses if they are in the same location.