Pure naivete. You don't have to destroy your enemy to win a war
In traditional wars where the enemy has territory, requires resources and has to maintain a supply chain, sure but this is not such war - you have an enemy who can turn invisible, teleport and outrun bullets. Again, giving the reapers all these capabilities in Arrival made the war unwinnable.
When you're not able to repudiate an argument
Citing wikipedia is not an argument.
Of course I'm assuming detonation on the Reaper hull. Why would I detonate anywhere else?
Because nuclear missiles are slow, and waiting to detonate them only after impact maximises the chances of the missile getting shot down or dodged. Again, if the reapers can see the nuke they can jump to FTL and escape unharmed.
In fact 50% might as well be 100%;
I have no idea what you could possibly have meant by that.
most other weapons have vastly lower efficiencies including railguns on a dreadnought.
I think you are talking about a different sort of efficiently because when you hit someone with a kinetic projectile which does not penetrate then all the kinetic energy is transferred.
What you may be thinking of is probably the power required to fire kinetic weapons vs power required to use produce/nukes, but since there so many unknown variables I don't see how you could possibly think that you can conclude anything with any kind of certainty.
If anything, the wide-spread adoption of mass effect based rail guns (using mass effect magic to get around conservation of momentum and energy) suggests that these kind of weapons are more effective than conventional ones.