IDR should be applied after Energy Shield, similar to how it works currently. The same goes for MDR.
Do note that both of these actually happen before any %-effect on damage. This means that resistances (including Conviction) and %-dr (from gear, Amplify Damage, Decrepify) do not actually matter for them at all. Also, MDR should be much more viable against quick attacks (FW etc.) in 1.09.
As for the Mercs, Barbs probably do more damage. However, the short leash makes the mercs pretty bad in dealing sufficient damage, at least in my opinion. Crushing Blow should be highly useful against bosses however, if they ever get a single hit in.