I created a special escort, I took a small hull and loaded it with beams. and engines and gave them a smidgen of Armor. I produce 2 for each Survey ship and so far as a fleet they fly to the anomalies and have been beating the pirates and getting the goodies. 

As the Terrans all of my survey ships have weapons and while it seems I am only getting the warning on manual survey, the only way I have lost is when my hit points are eroded to about half. The weapons work fine in the battle viewer.

With a custom race my surveyors show that they have weapons but you can't tell from the battle viewer. The just fly around taking fire and they win about 50% anyway.

Weird, go figure?? It obviously needs some work. I also did the fleet thing exactly as Larsenex and that does work well, plus the fighters get the surveyor bonuses from the graveyard anomalies.

And I am playing a custom race I based on the Terrans.