At present, missile engine efficiency is really a bit of a joke. With a TN start and automatically assigned RP, a size 50 res 1 sensor will spot an incoming missile at 5m km. At the same tech level, a size 1 missile with 0. 01 (1% of total size) devoted to fuel will have a range of 6m km. Devoting 10% of total size gives you a multipurpose anti-ship and anti-missile, with only a minor cost to performance.
By making missiles (especially small missiles) more fuel hungry, the efficiency bonuses conferred by larger engines will start to make an impact and we'll have to make real tradeoffs between range and quantity.
I think you may be comparing the wrong thing. Early missiles are generally performing very bad.
To get good performance on missiles / Anti missiles you need maximum power modifier.
When using x 6.0 power mod fuel consumtion is increased to be 88.18 times the standard specified amount.
When I try out the same thing with max power mod I need around 5% size dedicated to fuel to get 5mil KM range and making a multi purpose missile with 100mil km range is not feasible with such a fuel thirsty engine even with 50% fuel. (50% fuel gives me around 60mil km range).
I agree that missiles could be even more fuel hungry, but not by any radical amounts.