I think the idea behind the Antaran raids is to provide a temporary shock to the player. When they show up it disrupts whatever was going on at the target world for 3-6 turns, as you scramble to evacuate, and another few turns after that to re-establish yourself.
I actually like that they use biological weapons since it makes the costs of the raid more manageable. You lose a minimum of 1 population (potentially more if you botch your evacuation or get caught with no cash on hand), you lose the buyout cost of the civil transports, you lose whatever defensive structures you had in orbit. And of course you lose time.
It's also interesting in that this mechanic basically forces the player to make use of civil transports, at a point in the game when they might otherwise ignore them entirely. Usually I take the Antaran raid as an excuse to disperse population.
All that is just to say, I'm not sure how much of a real threat the Antarans are meant to pose. The feel more like a sideshow, and challenge that the player is supposed to face more at their own discretion.
I guess I wouldn't mind conventional bombs, the situation would still be similar, you'd just have to scrap all your structures while buying out civil transports.
I think if the goal was to make it truly a nightmare raid, the Antaran target needs to be totally randomized, rather than going after the system closest to the players largest fleet. If the player can coax them into appearing at weak systems, then they can metagame the raid to minimize the damage.
Again though, I'm not sure if the Antarans are really meant to take center stage like that. They'd be pretty frustrating, at the current doubling ship scale, if the raid happened at your homeworld and destroyed all your advanced infrastructure etc.