The first survey ship in Galactic Civilizations III is armed which is helpful against pirates hanging around junk yards. However even with the Militarization technology the new ships aren't being made with offensive capabilities. How do I arm my survey ships so they don't show up unarmed and naked to a galactic gun fight?
The first survey ship isn't a survey ship per se, but your "Flagship", it is advanced in most categories; Weaponry, speed, higher HP allowing it to handle early pirates before you get that capability on other vessels.
If you want a survey ship with weaponry, you have to design it yourself in the designer. Equip a ship with the survey module and weapons. Done. You need the space weapons technology to get access to basic weaponry. You may also need the tech for small sized ships, I'm not sure a tiny ship can carry a survey module + weapons.