The principle is that missiles are area attack weapons while energy is precision. Against ships, missiles cause damage via near misses while energy is a direct hit.
Therefore, missile AP pattern must be more, more flat - it must sandpaper nearest half of ship's armor, not digging out a crater (and this rule is also even simpler, than VB6 WH AP pattern rule).
Also, nukes in space are far less powerful than nukes in atmosphere (well, less powerful in heat/blast but more powerful in radiation terms)
They are not, really!
Atmospheric blast wave is very weak and soft comparing to blast wave, stamped in the hull by an instantaneous absorption of x-ray wave and, correspondingly, instantaneous
thermal expansion of these layers of hull. In truth, vacuum blast will be delivered to a hull sharper and less weakened by medium absorption, than atmospheric blast. Do you remember Honorverse laserhead blasts? It is the same, as a blast of nuclear near miss - it's not a
slow warming up and degradation of an armor. No, it is
instantaneous warming up, when outer layer (1cm or 1m layer, depends on the power of warhead and distance) of hull is just transforming instantaneously into an overheated mass - plasma, gas or simply heated armor - and then hummer inner layers with a deadly sharp shock wave.
Look at it from the other side: in vacuum, energy of nuclear blast spreads as a near-spherical wave, and therefore weakened with 2nd power of the distance, while in atmosphere this energy is quickly (comparing with air blast front expansion velocity) redistributing by air reradiation, so it spreads near-uniformly by sphere
volume (of the blast sphere), and therefore weakened with 3rd power of the distance, and wasting mostly (99+%) to the mushroom cloud heating and lifting (that is spectacular, but not dangerous for most of this warhead's targets).
Vacuum is an
ideal medium for nuclear blast damage! It just spreads there more sharp, less stretched in the time, less distracted at the
medium (not target) heating, shaking and degrading, and so on.
I don't want to have a situation where a ship with a single laser can wipe out an entire civilisation from orbit without any cost, allowing your own colonists to move in the next day. The game play rationale is that while a single nuke could take a out a city, energy weapons are designed to hit specific, small targets.
Well, would you like to introduce weapon overheating? It can be represented by very simple rules. For example, overheating time = const * capacitor tech.