One entropic strike affects one vehicle at a time, so I can't see how it can reduce all vehicles in the squadron.
As to who allocates successful entropic strikes on the squadron, it can be argued that it does not count as wounds nor glancing/penetration hits on its own, so it is unknown to us whether you can actually allocate it by either players.
Logically, since you can't allocate hits to which vehicle in the squadron, I would house rule it to count as entropic strike "wounds" suffered. However, the player controlling scarabs would in all circumstances can't choose to allocate things against a unit/squadron except for when there's independent characters or special rules allowing.