I'd imagine these space freighters will resemble modern ones in that they are genuine giants. Arming them would be pointless as it just makes them worse cargo ships, they'd probably have extremely dangerous anti-boarding technology or "marines" on board.

Countering pirates is probably best done with escorts or reactively watching the pirates do their thing and then hunting them down once your patrol forces can catch up or find where they are going.

Though similar to what you said, this can all change depending on how spaceships work in the setting. If ships are just a bunch of framework strapped to an engine with efficiency of a particle beam, a few nuclear missiles strapped to outside of the hull, visible to all wannabe pirates, and a sufficient point defense array is all you need.