Hmm....don't ALL ships now sometimes take a bit of damage from powerful weapons even with shields up?
I think that's the result of upping the weapons damage...Or it might be some weird side-effect of something.
As far as disarming the cruiser - you'll find Rockeyes can take out the anti-fighter beams with ease...and from great range to boot. With the latest fix file, you can call in a reinforcement wing too.
Regarding the secondary bank capacity - that was deliberate given the different balancing. The HOL don't use as massive numbers as shivans usually do, but their pilots have higher AI settings. Having the player rely more on primaries and actually dogfighting a bit more drives the point home better methinks.
If you think you're having a hard time now...wait for DOTA...shivan fighters/bombers and weapons got a considerable beefing up.