The reference to the extra 5d6 is with the star which is beside the nuke and not the HE missile, also the line mentions radiation which is why I think it refers only to nukes.
It makes sense to me that a nuke is going to be more damaging than anyones HE even tech 15 stuff.
As to why d6 vs d8/10/12/20 etc. I don't know. Damage variety is a good idea but the numbers don't make sense.
A meson hit doing d20 against a missile doing d6. The meson is a simple (well sort of
) explosion that happens to go off inside your hull ignoring armour, why it is so much more effective than a missile I don't know.
Also fusion doing d20 against a missile doing d6, a USP 9 fusion hit does 9D20, a USP 9 salvo of nukes does 14D6. Against an armour 0 target thats an average of 95 against 49 and against an armour 15 target you have possible max of 13 damage against a max of 4 damage.
The problem as I see it is the d20s, d6/d8/d10/d12 gives a good range without massively overclassing the lower dice.
Try Nukes/fusion/meson at D12, the rest as they are and either adding 5d6 to any missile salvo or not using it at all.