I didn't spend a whole lot of time testing it, but what I found in a quick and dirty was if I just spam fired and left my pets on auto attack, the scorps were better. If I actually tried aiming the bops and making them decloak/alpha strike, the burst of the bops was still "better". I wasn't parsing, I turned my KDF to a fun time alt, sorry.
I once again match my character. Behold the power of PINK!
My experience is that if you plan on running high Aux and have flight deck officers, get Scorpions. You can get the launch time down to 10 seconds, and since pets reset their tactical abilities on every launch, this equates to huge quantities of heavy plasma torpedoes flying everywhere and obliterating everything.
On the other hand, if you plan on running high Wep power and no FDOs then go with the BOPs. They need a firmer hand on the reins but have a lot of firepower and are less reliant on launch-spam since they have better endurance under fire and higher inherent weapon damage.
Scorpions: high aux launch-spam and chaos.
BOPs: low aux targeted precision strikes.
Though, something else to keep in mind. BOPs can only be used by the Vo'quv. If you ever want to try Recluse or Dreadnaught carriers, you can't take them with you. But scorpions are not tied to any specific ship.