Imo its hard to beat a size 1 magazine.  It is incredibly hard for a size 1 magazine to explode and take out the entire ship.  Where as the bigger the magazine gets the easier and easier it gets and even with armor it can still happen from just one point of damage.  The only real problem is Mesons but if they are close enough to use Mesons then your missile armed ship is probably already dead so why waste space on armor.

Note this is just for magazines on combat ships.  I don't know how I would handle colliers if I were to design a magazine just for them.

Can a secondary explosion cause a tertiary explosion? If yes, small magazine may be more dangerous, as having one take a hit means it'll get destroyed, and likely destroy more magazine, that can destroy even more magazines...

As far as I know, yes it can create a tertiary explosion.  Even so, on average there will be no difference (assuming they're both HTK1 and you've got the same capacity in both cases) in the damage done by tertiaries in the same set of magazines.  It all comes back to the fact that both the large and small magazines are HTK1.  Let's say we're comparing 10 size-1 magazines to 1 size-10 (both HTK1), and let's say the secondary explosion strengths are 10pts and 100pts respectively.  If a small magazine is hit and explodes, then it's the same thing as the ship taking a new strength 10 hit from a bad guy weapon in a spot with no armor (i.e. all interior).  The ship still has 9 magazines left - even if all of them are hit and explode (a VERY low probably - if explosion probability is 0.1, then you've only got a 10^-9 chance of all 9 blowing up) you'll only generate an additional 90 points of secondary damage, for a total of 100 points of secondary damage.  If a size-10 magazine is hit and explodes, you take that 100 points of damage immediately, and there aren't any extra magazines to soak up hits with their HTK.  Note that for an explosion chance of 0.1, one of the size-1's exploding will do on average 1 point of damage (10pts * 0.1 chance), while the size-10 does 10 points of damage.  I just realized this is interesting - since both are 1HTK, the size-1 is effectively 0HTK on average (it absorbs 1 hit, but on average will blow up doing a hit of secondary damage) and the size-9 is negative 9HTK (it absorbs one hit generates 10 in secondaries).  It just occurred to me that magazine clusters with negative effective HTK are like atomic bombs - they're susceptible to a chain reaction that blows all the magazines up.

John

Can a secondary explosion cause a tertiary explosion? If yes, small magazine may be more dangerous, as having one take a hit means it'll get destroyed, and likely destroy more magazine, that can destroy even more magazines...

Note that while cost and hullspace scale linear, personnel needed does not - larger magazines need less personnel than smaller magazines for the same amount of magazine space.  More personnel means more hullspace needed for life support.

Are you armoring your magazines?  Because if not, then the cost of 20 size-1 1HTK magazines appears to be identical to the cost of 1 size-20 1HTK magazine.  In other words there is no cost savings.  Again, if you're armoring up, the story's different.

[pause while playing with magazine design screen]

Ok, even with armor, it seems like size-1 is MUCH better to achieve the same HTK.  First, the selector only goes up to 10HTK.  So if you're at size 10 or more, it's impossible to get more total HTK than using an equivalent capacity of size-1.  Second, the capacity for the same total HTK is smaller for a big magazine (and hence the cost is larger).  I just compared 5 size-1 HTK2 (w/laminate composite armor, efficiency 90%) to 1 size-5 HTK10.  A single size-1 holds 17 points and costs 1.61, so 5 of them hold 85 points and cost 8.05.  The size 5 holds 70 points and costs 15.79.  The size-1 magazines are superior in all respects.

I've decided to log this as a bug....

John

To be truthful I haven't compared the costs after the last changes to magazines.  Add to that I'm working from memory since I haven't had time to play since mid February (employed again yay!!)

But the part about reduced secondaries should still hold true.

But doesn't the ammo explode when the magazine is killed? Unarmored magazines are a secondary explosion waiting to happen.

As Brian said, compartmentalization.  It does increase your 'hits to kill', but the real benefit is reduced size explosions when they are hit.  The downside is increased cost per ship.

My design philosophy is to design a magazine that supports the salvo count I want a launcher to have.  When you add a launcher you add a magazine.  Counter Missile magazines usually have storage for 75 missiles at size 1, anti-ship missile magazines usually have space for 20-30 size 4-6 missiles. 

Magazines for colliers I do differently.  Those I make much larger since they are not intended to be in the direct fighting.

Oh damn....I've been giving a magazine for every launcher!!!!