If I use Houndstone ex's "Last Respects" attack, would I count each piece of Mewtwo V-UNION in my discard pile as a separate Pokemon?
Yes, each piece will add to the damage.
Source: Obsidian Flames FAQ; TPCi Rules Team (2023-08-10)

Relevant cards

Note: All applicable cards may not be listed below.
SV3_102
SV3_102