This is directly addressed by the general
FAQ, under the subheading "Blast Markers & Templates", top left of page 14.
Q: In the case of a template weapon that fires two or more times (such as the Blood Angels' frag cannon), do they still only inflict D3 hits when firing Overwatch, or D3 hits per number of shots int he weapon profile?
A: Always D3 regardless of the weapon's profile