Apparently I'm unusual in that I use my Jemnaught as an artillery platform rather than a cannons platform.
Front weapons are dual beam, beam array, and 2 photon torpedo launchers. Rear weapons are cutting beam and 2 turrets. 3 projectile officers and 2 flight deck officers on duty. I have High Yield 2 in both tactical LT slots, then APB2 and APB3 on the higher slots. 2 disruptor coils, 2 photon detonation consoles, plus the KHG 2-piece bonus to torpedo damage.
I just sit waaaaaay in the back and spam torpedoes and fighters, while my APB keeps the target taking elevated damage from everything thrown at it.
One thing to note on my skill builds that I posted. I use that build on 5 different ships. A fleet bop, the carrier, the bug ship, a fleet vorcha and a krenn. So it is a bit of a generalist build. The 9 points in stealth dont do much for the carrier. But I live or die by not being seen in my bop.
The elite scorpions are better and it's not really close. A few people I know run the advanced JHAS pets and they average ~1.5 DPS/hanger when I've parsed it, I run elite scorpions and they average ~2.1-2.2k DPS/hanger.
If we're all on a combat parsing lark, do remember to make sure that Elite Scorpions are getting credit for their heavy plasma torpedoes. Because the torpedoes are an "officer" and not direct damage caused by the fighter, some parsers can put them into their own category.