To be honest if you play against the AI there is no real need to try and game the system since the AI can never react to such designs and you are perhaps just making it too easy for yourself (my opinion). If you did it against a human you would in general be up against a layered defence which could deal with it more efficiently. Secondly it is much cheaper to armour your missiles than using small decoys. An armoured missile are allot cheaper than the one that contain a few decoys. If your main missile is larger than size "6" then you also encounter the problem that it will be visible by the enemy much sooner then your smaller decoys and so can potentially be fired at long before they either deploy the decoy or before the decoy is ever detected.
A size 10 missile with two points of armour have the same chance to survive as if you put two size one missile decoys in it (unless the decoy is much faster). Each missile that hit it has a 0.33% chance to destroy it. In reality systems would probably be intelligent enough to concentrate their AMM fire on the biggest missiles first and the smaller missiles last, so it is almost like cheating to use a flaw in the game mechanics against the NPR...
...everyone can do as they think is fun and neither way is wrong, but simply putting armour on the missile will generally be cheaper and easier to do.
If this was for real I'm pretty sure a ship could fire a very large salvo from regular launchers and then all missiles would merge into one single large salvo that arrive at the same time. It would not be very hard to program the missiles for go slow in the beginning and wait until all missiles travel together (more or less) and then arrive to overwhelm the enemy defences. Things like this can be done today so I see no reason why it would differ in the future.