I'm afraid exelsis is correct, that is a programming thing, not something encoded in the modifiable XML files.

However, you might be able to get the same effect: you just have to find the part of the XML for each weapon and defensive component that controls the 'type' of weapon. I suspect it is the bold item here:

<ShipComponent>
<InternalName>SingularityDriver</InternalName>
<DisplayName>SingularityDriver_Name</DisplayName>
<Description>SingularityDriver_Dec</Description>
<ArtDefine>WeaponModel_05</ArtDefine>
<Category>Weapons</Category>
<Type>KineticWeapon</Type> [...]

Change all of the weapons components to kinetic (or whatever), and change all defense components to the corresponding defense (armor in this case). The effects will still LOOK like beam and missile weapons, but all weapons will be blocked by all defensive components. One problem will be that the statistics and tooltip summaries will only list the ships as armed with kinetic and defended by armor, regardless of the special effects. I assume the AI won't have a problem with such a mod, but I'm not sure.

If you do this, be sure to change all the weapon augment components too, because the beam and missile and shield and point defense augments obviously won't work if everything is kinetic and armor. You should probably also take out the components that allow kinetic effects to ignore armor (assuming you modded the components to kinetic), since ships with those components may be very unbalancing.