already explained in Best of Both Worlds, Shelby and La Forge were discussing anti-borg tech and Shelby projected 24 months before they'd be ready, that was 8 years before First Contact.
Voyager was able to pull plenty of random crap out of their asses to save the ship and the day (the plot reactors didn't work all the time, remember), and add to that, Starfleet had a lot more info on the borg after the BOBW battle, whereas they only had the original Q-Who encounter the first time.
Easily stands to reason that some of the theoretical anti-borg tech that Shelby's team worked on was brought online and at least partially successful during the battle, which would explain the damage.
As for the comments on "weaknesses", there aren't _meant_ to be any, that's why they're cube shaped. If memory serves, the draft of the script explained the vulnerability that Picard targeted as a ship having crashed/rammed into that area breaking the outer and inner hulls (Maybe it was supposed to be the Defiant before Behr complained, I don't know). So in FC, I argue that the weakness they aimed for was just a hull breach caused in the battle that Picard listened in on to find out was easily exploitable.