I tend to design incremental upgrades of what are essentially the same missile systems in game. As my base warhead technology impoves for example I might take a previously designed size 4 missile and use the new tech to achieve the same damage with less mass. I would then use the weight savings to add more fuel, a larger engine, more agility, etc.
The design philosophy of the missile remains the same. I would like to be able to take missiles and remanufacture them to the new standard.
The only part of a missile which has no tech changes is the fuel, which means maybe 90% of your missile would be replaced.
The old warhead gets swapped for new warhead, the old agility gets swapped for new agility and the old engine gets swapped for a new engine.
What you are proposing is completely different to refitting a ship, where the majority of the ship stays the same.
Secondly missiles are disposable so I don't really see why you should be upgrading them.
I could also see the argument for having a construction option called "recycling", where you build missiles and scrap them at the same rate to make the missile effectively cost less.