Okay, I've run some tests, and there is definitely something not working right. However, this is also the case in the unmodded game.
I've modified the UPIssues.xml so only the Armed Transports proposals are in it. Within the game, I used the cheats to force a UP meeting and voted for 5 pts. I then gave myself the techs Planetary Invasion and Interstellar Construction, and built troop transports using both the stock design and a small hull-based custom-design.
I then unveiled the map, and picked the closest race. Both designs had no trouble destroying unarmed ships. Armed ships, on the other had, always destroyed both troop transports designs. The combat-animations played, but the transports did zero damage. In one of the tests using the otherwise unmodified game, however, I noticed that the transport managed to do 1 point of damage. So, they actually do damage, but just get extremely poor rolls.
I then began another round of tests, using the CU mod. This time, I gave myself the 25% Luck bonus. The troop transport now did consistent damage. Exactly 1 point per attack. Mind you, this was with an attack-value of 5 in all three categories. The minimum damage should have been 3 per attack. The damage was also never higher than 1.
I suspect that there are two issues at work:
1. The UP proposal adds the attack-value only to one of the damage-categories, even though it shows and says something different. The GalCiv 2-engine is a modified version of the GalCiv 1-engine, which only had one damage (and defence) type, so it is possible that this UP issue just didn't get updated properly.
2. There is something wrong with the damage-rolls for this type of attack. The amount of zeros I rolled was just unrealistic. I also never got anything better than a 1, even thought the max attack-value was 5.