I think the Widowmakers are supposed to be next-generation super-missiles, basically pure nightmare fuel for anyone the GTVA wants to kill. It is an antimatter missile after all. Antimatter weapons are almost always going to outperform non-antimatter weapons by a pretty huge margin. It's difficult to beat E=MC^2, especially when it operates at 100% efficiency.
Heck, the Widowmaker might even be using a matter-antimatter reaction along with some plain old reaction mass to produce thrust - which might explain why it has such awesome range and maneuverability. There are very few things that can theoretically be as deadly as an antimatter warhead propelled by an antimatter rocket.
In regard to "The Royal Fleet" balancing, I am not sure if it is possible to have different weapon quantities available for different difficulty settings. But if it is, I would give the player 100/90/85/80/75 widowmakers, for very easy/easy/medium/hard/insane, respectively. Or something like that.
This way, playing on Insane, the player will still have to fight 25 dragons with 'conventional' weapons, after expending all their Widowmakers. That will even the odds a bit, but it will still be a ludicrously challenging fight.