Straight up fighting? You should probably prefer the H6:20. But not for the reason you might expect.
The ships can reasonably expect to die at the same velocity. Even simple pulse improves by CAF (or, very commonly, twin-linking) substantially. 2-try pulse v H6: 30.56% hit rate. Expected number of dice to kill = 20 /.3056 = 65.45.
We can try this with 30 and H5: 55.56% rate => 30 / 0.5556 = 54.00. That's a 65.45/54.00 = 21.2% improvement, but hardly what you'd expect from Hull 6&20 vs. H5&30 against simple pulse, CAFed or not.
Your gut, Rynar, is spot-on at the Nova: 36/0.5556 = 64.81, right there with the H6. The bigger ships even get better advanges when you notice the assymmetries between crew and damage allows for use of CBD, which dramatically improves your staying power for one turn.
Against AP, CAFed or Twinned, H6 is worse, of course, but against beam it's better (now, mind you -- many beams out there are SAP, which really eats into H6's advantages).
But ... the other thing that must be considered is that there are three ways to kill a ship. One is to take a score down to zero. Another is to critical it into irrelevance. A third is to board is and own it. The last is to force it down with Stand Down and Prepare to Be Boarded. The third largely is the second, as you have to have your target stopped, and the only surefire way to do that is to get a 1-6, 2-6, 3-6 critical. And while the damage likelihoods stay proportional to the hit rate (and, as seen above, pretty close to their damage thresholds, espeically when you factor AP weaponry into play), the special effects on ships are NOT proportional. They aren't linear like damage is, is a Heaviside distribution, it is or it is not. And those non-damage dependent effects are mandatorily easier to get against H5. In particular, the difference to Drazi between H5 and H6 is spectacular, as there are so many criticals out there that can be relied upon to deny your boresight any shot at all --- 1-6, 2-6, 3-6, 4-5, 4-6, 6-3. The assymmetry remains that H5 is far easier to accumulate critical events upon than H6.
This could be reasonably offset if Criticals could be erased multiple at a time. Unfortunately, this ability is a crew check at difficulty 9 (any predominantly H5 ship user should read All Hands to Deck! before every match. I've seen far, far, far too many people forget this order existed. There's more to life than CBD and CAF!) to get off. This often leaves you repairing one system at a time, a slow and maddening clip. Hey, if you've launched your auxilliary craft and have to turn, at least this order costs you abosolutely nothing at all to execute.
Similarly, if the H5 ship had some other ability -- ignore one critical event (not the damage) every three hits, that would change it all, too. But, it doesn't, and those lovely H5 ships parked on crit-stoppers will continue to taunt us.
Note, of course, that as the ships get smaller and smaller, this becomes less and less relevant. You get critted at Skirmish and lower, you cease to care so much about losing arcs and attack dice and just want to concentrate on living! This is the inverse of the "big-ships-live-and-die-on-crit-rolls" phenomenon.
So, there needs to be some additional enticement, even beyond 30 damage to 20, to get you to H5 instead of 6.