Yes, I reconed.
The weather was clear in the first day, overcast in the second.
Average ground attack skill lvl was 70+.
I think all factors favored my bombers. I think they should have obliterated the enemy bases, but for some reason, they didn't.
I forgot to ask the most important question in the OP...
In the hypothetical scenario of Japan conquering most of Australia, north of the trigger line, and thus being in range to attack Australian industry, do you think Japan could achieve decisive results, in terms of victory points earned by disabling or destroying industrial centers?
Re the bombing I'd keep trying. LI is harder to hit than HI in my games. More dispersed. Maybe you got some bad rolls. Also, the size of the city in th ehex, or lack of size, might be in there too. I'm bombing Chinese LI in my 1942 game and I only get a 1 point hit maybe every three missions. Not with Helens, but it's still directional results.
To your second question, open a game as the allies and count VPs. If you want VPs for taking the big cities like Sydney and Melbourne you're going to have to cross the line.