Sins often takes several seconds to show any damage on the health bars in the normal game, so this is probably completely normal. I don't think there is anything you can really do.

You can try it, but I think you are still going to get some delay. Even constant damage effects like radiation bomb don't show up instantly on the health bars, and even with dozens of ships focus firing it often takes several seconds for the health bar to change. However, this delay only seems to effect the visual aspects of the game. I've noticed that the unit AI will stop firing on near destroyed enemy ships several seconds before the ship actually explodes, so it seems that for game mechanics the health bars are updated instantly, we just can't see them...