I'd go with the young ships - the quad damage slicer on the ancient is cool and scary, but is not anywhere near double the firepower - nor does it improve its range.
Equally, double the hitpoints but half the numbers adds up to no net gain*.
Shields are doubled, but self-repair is not.
Two young ships have the edge tactically because you can split them up and send one down each flank for crossfiring slicery goodness.
The big suggestion I'd make is pairing some or all of the scouts up to stalkers (max of 4). A shadow scout does 4 things
1) Initiative sink - but you don't need to line up boresight weapons, so this isn't critical
2) Accurate weapon weapon - but wasting a phasing pulse cannon on centauri fighters (whose antiship weapons are pitiful) is borderline criminal
3) Stealth breaker - but there's only one possible stealthed target worth worrying about - the Dargan-class strike cruiser, and you have an innate stealth bonus anyway. His own scouts are low priority for the same reason as neither twin-linked ion cannons nor beam battle lasers benefit.
4) Reroll generation - which doesn't work for any weapon except the scout's own guns!
One pair of scouts might be nice, to go hunting for liatis or dargans if they do show up, and to give a shot at the magic initiative reroll. No more than that, really.
That works out at
1 Ancient Shadow Ship
2 Young Shadow Ships
3 Shadow Stalkers
2 Shadow Scouts
* In a one-off game. In a campaign, where any surviving shadow ship self repairs at no cost, the big boys rock.....
