When I use Roxie to discard two Pokemon that each have the "Blow-Away Bomb" Ability, do those abilities stack so I can place two damage counters on each of my opponent's Pokemon?
Yes, each of the Pokemon gets to use their own "Blow-Away Bomb" Ability when discarded by Roxie.
Source: Cosmic Eclipse FAQ (2019-10-18), TPCi Rules Team (2019-10-31)

Relevant cards

Note: All applicable cards may not be listed below.
SM12_205
SM12_205
SM12_243
SM12_243
SM12_76
SM12_76