I saw someone else complain about pirates in Beta 5 opt-in patch 3, and I have to agree that I think they've been beefed up more than a bit too much in the latest patch.
First, some background. As I understand it, one of the reasons a faction's initial survey ship was given both offense and defense was so that it could be able to scan the occasional pirate infested anomaly and survive. From playing around in patch 2. I found that my initial survey ship could take on one, maybe two, infested anomalies before having to rest up and repair. Which was fine by me.
In Patch 3, however... Well, just see for yourself:
Yeah.
Now it is true that I am using a custom faction that is (more than) a little weak militarily (they're Fragile, Inaccurate AND Brittle [Don't Ask 
]). Still. Still with the exact same setup I was able to hold my own in at least one or two battle(s) in B5 patch 2. Here though while I am actually able to kill one of the pirates in that combat picture above, I eventually get blown out of the water. So to speak. 
For comparison, the pirates that are being generated at pirate bases aren't nearly as strong at the beginning of the game with attacks and defenses in the low single digits.
For further comparison, I managed to figure out what the anomaly protected pirate strength was in patch 2 by loading up an old save where I was testing a custom built cargo ship against pirates to see if it would survive (it didn't, but that's why it was a test).
The pirates, being pre-generated, weren't affected by the patch. So that lets me do a direct apple-to-apple comparison:
As one can see there is a teeny, tiny, difference between Patch 2 Anomaly Pirates and Patch 3 Anomaly Pirates. Just a bit.
So while I appreciate making them tougher, I think it went a bit overboard. 