how disruptive is adding a crew "value"?
You could generate a number of crew hit boxes based on hull, weapons, etc.

And why didn't we play Iron Stars when I was with you guys?
*hurrumph*

Could you have non-hull hits by poison gas or other crew casualty inflicting weapons (IE -- if it hits the secondaries, primaries, light guns or armor) simply be ignored?

The reason is that a large explosive round can take out a weapon or damage the ship's thrust without actually piercing its hull and exploding deep in the guts of the target.  For engine hits, maybe the sails are damaged, or the screw warped.  For weapons, hell, the turret's jammed, the external portions of the weapon blown apart, whatever.

But gas is only good if it gets inside the ship.  So only apply its damage if it lands a hull hit.

Originally you were talking about having a set number of crew boxes based on hull size (Hull/2?)

You can mix some ideas.

Have crew-targeting weapons roll on the target's damage track, but anything other than a hull hit is ignored.

The fact that you only have half as many crew boxes as hull bits, though, means that when the shells do penetrate the hull, they hit twice as hard.

This way, VS ships would die after taking 1 to 2 crew hits (we'd be talking 1 hull/2 rounded up all the way to 3 hull/2 rounded up).  But achieving those hits would be a little harder than the way it is now. 

A small ship like the Tycho could take 3 such hits (5 Hull/2). 

The Gauntlet could take 10 crew casualties (19/2).

This way, VS ships are still killed by at most 2 crew hits, but by getting rid of the "automatic" damage previously seen in poison gas, you make it less likely to happen.  On the other end, heavier ships will have to view poison gas and other crew-targeting weapons as more of a threat.

I found that, on the whole, poison gas is vastly more effective against smaller ships, for these reasons:

1) In the Merchant War, most of the gas guns are short-ranged. When I played the last scenario, the British Orpington, a whale of an ether-ship, was able to keep its range and blast the poor gas gun-armed ship into smithereens. Smaller ships can't mount the weapons as seen on Orpington, and mainly mount torpedoes which are extremely short-ranged, thus allowing a gas gun-armed ship to give these vessels 4/6 gas guns each and kill the crew.

2) vessels such as the Alpha or Gamma only have 2 hull boxes. One hit from these guns and WHAM! your crews dead or half-dead. They also have weak armour, which both allows the gas guns a chance of penetration and increases the range at which these weapons can engage. Three destroyers were lost this way, as they closed they were outside of torpedo range, but inside gas gun range and they died.

I have no suggestion, however.