1st time poster yo.
I bought the original AE boxset when it came out, the 3 mini-boxes from a RightStuf sale when I was worried about the Macross liscense disappearing (these I keep meaning to ship to a friend), and finally the repackaged HG set when I couldn't resist the artwork on the box (at the time the HG box was still $99.99, so I'm a real sucker).
As far as I can tell, The HG discs are identical the the AEs, just repackaged. And are just as prone to cracking.
Last time I watched Macross I did not notice any 'cracks' per se, but definitely some signs of seperation along the hubs of the discs. I suppose it's possible the discs haven't changed since I bought them... really couldn't say.
I take pretty good care of my DVDs, as much as is possible considering my living conditions (there was an extended period last summer when my appartment management was slow to respond to various air conditioning problems I was having... who knows how much the lifespan of all my DVDs may have shrunk during that time).
Here's what I think:
Depending on how concerned you are, you might buy the HG set as a backup ($40 isn't a lot, all things considered), keep it unopened, plus have someone backup DVD-R copies of your current set for you.
And that's the most I would recommend. At some point, you gotta shrug your shoulders and figure you only have so much control in life anyway.