My balance concerns are not about missile vs beam, but about large missile ships vs multiple smaller vessels. If magazine explosions become too lethal, especially to unfortunate lucky ships, it just gives a huge incentive not to use large vessels. Currently the only real advantages to using very large vessels is increased survivability, but with the changes to shock damage combined with this, that may be reversed. That means that the increased logistical problems related to running larger vessels, like needing larger tenders, larger shipyards etc, will have no real payoff.
Additionally, from what I understand reactors usually make up a very small percentage of a beam ships tonnage, making lucky shots possible, but unlikely. A missile ship however can regularly run with 20+% of its tonnage as magazines.
I am sorry to insist, but you are completely ignoring my argument that a missile ship's main defense is being far away form the action, and just insisting on the magazine thing. Which is pointless by itself, because it has to be considered in the whole context, not by itself.
This possibility of your ship blowing up just from small damage ONLY happens with mesons. That means, meson fighters or meson warships. If you let a meson ship in range of your missile ships, your entire war doctrine has completely failed. Missile ships are made for long range engagements, if you let something with mesons this close, your military is inadequate.
In that case I see no problem with the fact that you are risking death. In fact you should, because you have failed. And you can still build magazines with a 90% ejection chance and a high HTK as written above, to lower the chances of unlucky hits. And large ships should always have an escort, and anti-fighter defenses as well. So yes, can happen but unlikely to do so. It seems perfectly reasonable to me.
For any other kind of damage, be it long range missiles or any other kind of direct fire weapons, all your defenses apply. So the large ships will have a proportional advantage, compared to the smaller ones. Plus the aforementioned better magazines. Plus the fact that you SHOULD be far away, and so that you should kill your opponents before they get close, and have an escort just in case. So once again, if the magazine explosion thing happens, your war doctrine has failed or you were outgunned to begin with.
Ultimately, unless you are outmaneuvered/outgunned/outresearched, the chances of this happening are really very low. And war is NOT meant to be some kind of exact science. Just having a large ship should not make you immune to everything and anything.
Once again, real world reference. If you let an old, decrepit Word War 2 battleship, or any submarine, close in to ANY modern missile cruiser or carrier, I assure you the missile cruiser/carrier will be sunk in SECONDS. Range is their main defense.
So bottom line, yes I am in favor of both 100% damage and proportional explosions based on how full the magazines are. Because using missiles has to carry the realistic risks it implies.