Strange ship capture thing !

[Suicide Junkie]

That quirk has apparently been fixed for Gold...

What you can do in the meantime, is create really fast capture escorts, with boarding parties, and a second warship design loaded with shield depleters/disruptors and a meson bLaster.
The warships should have optimal range as a strat, the escorts "capture ships".

Once the shields go down, the capture ships will zoom in and take the ships, hopefully arriving before the warships can do too much damage.
If you set the warships to switch to the least damaged target after doing about 10% damage to their current one, you should be able to do very well.

Note that this fleet would suck in most situations, and is only good for ambushes