1) I have no idea, but I think that because most ships only have one keel, they'd only have one keel bombard.

2) The Iron Stars rulebook specifically states that secondary batteries may only have x1 or x2 damage values. You could, I think, mount longer-ranged secondary batteries, but we're talking, primarily, about naval-style etherships, and no naval ship ever employed 9.2in guns as primary weapons and 12in as secondary weapons.

1) The intent is for only one keel bombard per ship.

2) Secondaries should have a lower damage value than the primaries.

Having said that, if you break both these guidelines, your ships should still be balanced.

I would let him stow his guns how he wants, as the fact that these are ether ships means they aren't necessarily going to follow traditional wet navy guidelines. 

Secondaries have limits.  You can't bring as many to bear on a target as you can with primaries.  If he wants to go that route, why not?  He's just dispersing his own firepower.

As for keel bombards and special kit, I bet you can use common sense to smell out a cheesy ship design.  If he's creating something JUST to be a pain in your a--, then don't let him do it.

Torpedo sizing is more of a design ideology, at least IMO.  The number a ship can carry is limited by the size of the torpedo vs space available, yes.  But that isn't necessarily the limiting issue. 

Example:  The Spaniards tend to use d10(x2) torps almost exclusively from other torpedo designs (at least so far) since they have a good hit chance, decent damage, and are space efficient to their way of thinking.  They could pack in a greater number of d6 or d8 torps, but these would be less accurate and shorter ranged from a generalized perspective.

To take a crack at answering the question about substituting torps with the Beta DD.  Yes, you could do that...with 1.2 SU left over for other things possibly, creating a variant Beta, though the points cost of the ship will need to be re-calculated since the offensive rating changes.

Short range, high damage torpedoes are great for FACs.

You move first, shoot first.  Capital ships can only respond after the fact.  So if you lurk outside of effective gun range until you're ready to race in there, you can essentially walk your torpedoes into an enemy hull at point blank range.

IE -- the Italian FAC published in Southern Front has two D6 (X4) torpedoes.

As torpedoes cut armor in half (rounded up), that means even an armor 5 vessel has the potential of being hurt.  An armor 4 ship, if targeted by torpedoes at less than 2", is going to be hit on a 5+.  Rolling two dice, that means you have about a 66% chance of drawing blood. 

Torpedoes also roll D12 on the damage track, which usually means all four points of damage are going straight into the hull.  You hit a ship that gives you three VPs per hull hit, and even if the FAC dies after its attack run, you've won more victory points than you've lost.

So that's the route I go with the attack craft.

With destroyers, I try and pick the longest reach torpedo I can.  I use destroyers to supplement the firepower of bigger ships.  And the longer they can reach, the more flexibility I have in deciding where to put them.  It's not really like destroyers can do a lot of good with their guns.

With capital ships, like the Hunyadi, I choose a torpedo that compliments its armor and guns.  With an armor rating of 4, the heavy cruiser is going to force most enemy ships to come within 5" to hurt it.  Around there, its torpedoes -- which are slightly longer reaching -- stand a chance of drawing blood. 

IS's fold up counters meant it was the only mini game I was able to buy and play in about the same day.  And it goes to the local hobby shop at least two weekends out of the month