There's some difference. I don't know what it is, but I do know that one of my raid ships will die quickly by itself on an AI world but one of theirs can happily waltz through my defenses right up to my home command station and eat it. Maybe it's some difference in armor piercing or... I don't know what. So the problem may not be in the ships themselves, but instead in the speed that one team can kill it over the other.
It depends what you're sending them up against. If the AI doesn't have anything that's strong against them, raid starships are brutally effective, because their high speed and decent damage lets them get in, pop a weak target (data center, warp gate, etc.), and get back out before getting hurt much. They can be really useful for that reason, even against things that aren't shielded. On the other hand, if the system is full of stuff like artillery guardians, your raid ships will get wrecked in no time flat. It's as hopeless as trying to kill a wave of bombers with a fortress.
In older versions, they were much more universally useful in my experience, but these days there's a lot more variety in enemy systems that requires different approaches to them, and some things are much more situational now than they used to be (like raid starships). It takes more work and more planning ahead, and it is more fun this way, but I do kind of miss my unstoppable raid fleet of doom sometimes...
Edit: Knew I was forgetting something. Raid starships are one of the units that benefit most from micromanagement, at least out of the ones I use regularly. They get massively more effective if you guide them by hand whenever they're anywhere threatening to them, because they're ridiculously maneuverable for something that powerful but aren't smart enough to take advantage of that on their own.