I know this is very specific and it's very minor and absolutely not game-breaking, but...
I put the Black Alert ship trait on my T6 Fleet Dreadnought. The trait works, but the cloned ships are completely invisible. I see the fun little lightning effect, I can hear and see the torpedo attacks, but there are no visible clone ships at all. I'm guessing that's because Saucer Separation is causing them to glitch out. Not sure there's anything that can be done about it and it's not super important, but if at all possible, it would be nice to see the extra ships. I don't know if any other ships are affected by this problem.
I can now confirm that saucer separation is in fact what causes the clones to turn invisible. I've recorded a video where I'm using Black Alert with the saucer attached and the clone is perfectly visible (at 0:59). Then I use saucer separation (1:43) and the clones no longer show up from that point on. Probably an engine limitation. Not sure anything can be done to fix that. On a slightly related note, Rock & Roll also doesn't work when the saucer is separated.
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Aforementioned video: https://youtu.be/QNrK_MyGnuw