I play at default and I have lost colony ships to them and it really ticks me off. But in a good way. My idea is yeah it is dangerous, and yeah I don't have time to baby sit every colony ship. So I try to use judgement to reduce bad things. I take a slightly longer route when I know it's safer. And so forth. I take the risk to hurry colonizing. And I am living with it, it sort of feels right. But --- the problem is that the game has a micro way to avoid it completely. Thee existence of that is a problem, not that pirates can be a pain.
So I agree with the OP to a point. Having the colony ship captain just be stupid is kind of ridiculous. I do it because that's what I think it should be like, I will take the hit. What I would like to see is that colony ships, or other non combat ships, have a small CHANCE to see the pirates, but no guarantee. Make soloing dangerous, something like but not exactly like Civ. So pirates have a cloaking rating perhaps. And ANY ship may blunder into them, but combat ships are less likely and ships with extra sensors nearly always see them.
It is too easy now to deal with pirates because you can see them a mile away and they move like snails. Now in real life pirates didn't have the best ships, they had what junk they could scare up or capture, and they depended on hitting the defenseless. When they ran into combat ships (like Blackbeard did in his last battle) it was generally curtains.
Pirates should have a decent chance to jump non combat ships, and a chance to avoid other ships if they are not smack next to them. But right now the game is making me be stupid or lazy to get the atmosphere I am looking for.
Of course people can escort colony ships. But then they pay a big price in time. That's appropriate.