Yea, these beam weapons actually lose strength as they do damage, so if there's some hostile in the way with enough hp the beam won't make it to the target. On the other hand, if it gets to the target, destroys it, and still has strength left it will punch through and hit any hostile behind it (within max range), too.
This is pretty different from the beam frigate and beam starship, which literally do a line-shaped aoe attack with equal strength against each hostile intersected by the line. It also just draws the line to the target, not to maximum range through the target. If I made the heavy beam cannons use this kind of attack I'd have to divide the attack power by some huge factor to balance it, and it just didn't seem to fit with the theme to have them be so weak.