The AC can be used with a TarComp, the missiles cannot.
The AC does 5 points of damage a hit, the missiles do an average of 3.
I'm not sure how the Jupiter would work with LRM-5s instead of ACs. Drop 4 ACs, add 8 LRM-5s and 2 more tons of ammo, now we've got 18 tons and two crits. Drop the ES and add four DHS, still leaves us with 9 tons and one crit. I dunno, I'd leave the ACs there.
ETA: Oh, and the ACs are much better in high winds.