[Q]

Your observation is correct and at the moment there's no solution to the problem.
The best solution IMO would be a line in the construction vehicle file, that prevents the AI from using a specific design once a specified tech level is available. Like that you could make a ship design for the early game with missiles but once he has lets say shard cannon level V, the AI will not use the missile design anymore.
If you want it to be perfect you could make even multiple tech levels as criteria for the use or not use of a specific ship design and combine them with logical and/or operators.
Another useful change in the hard code would be the possibility to include specific components in the design and not only abilities as it is today.