Unfortunately, not learning Atlas and Prometheus hurts if player relies on raiding for blueprints because unwanted and unknown blueprints keep dropping until you learn them. If you do not want to save scum blueprint drops, just learn them immediately after they drop.
Just put Phaeton and Colossus on priority, and your fleets will never use Atlas or Prometheus even if you know them. (If they do use them, I have not seen such a fleet yet.)
Learning capitals is worth it, especially if you can build pristine ships. Conquest is only 300k, and Paragon 500k. That does not include the free crew, fuel, supplies, and weapons that get shipped with a newly minted ship from your heavy industry. Buying one is much more expensive. Restoration, even more so (except for XIV hulls due to a bug).