So in my latest game there is a good chance that I'll be forced into using Laser warheads for RP purposes, so I decided to experiment to find out the mechanics of the laser warheads in a recent (5.4.2) version. For anyone else that may be interested, here they are.
As you progress through the Laser Wavelength tree you get to "Soft X-Ray Lasers". At this point after unlocking each new X-Ray wavelength you can next unlock the laser warhead for that wavelength. At this point you can design and build laser warheads.
Every MSP of warhead in a Laser Missile adds a new laser beam to the warhead, no fractions allowed. Each laser beam has a strength depending on the current wavelength of Laser Warhead, as follows:
Soft X-Ray Laser Warhead: 2
X-Ray Laser Warhead: 4
Far X-Ray Laser Warhead: 6
Extreme X-Ray Laser Warhead: 10
For some reason there are no warheads for the Gamma spectrums.
When the missile arrives at the target each laser beam rolls a separate chance to hit, and the beam hits are placed on the armor belt randomly, not on top of one another. Strangely enough the damage patterns are missile pyramids, not the higher penetration of the beam damage model. This is pretty much the only counter-intuitive result. Note that these laser beams only target the single ship being targeted. Regardless of the amount of overkill or whether the missile has its own guidance system. The missiles did no damage against a population in over 1 atm of atmosphere, nor did they increase radiation or dust. I did not test radiation or dust on a population with no atmosphere.
The Laser Warheads deal damage before the point blank defense of either a CIWS or a more general turreted laser beam PD. Manually targeting and firing at a missile at range successfully destroyed it. I was not able to get automatic point defense fire at range to work successfully on either a normal missile or a laser warhead, but I assume that it would have destroyed the missile as readily as manual fire if I was doing it properly. In addition the lack of any range setting on the warhead makes me assume that it is just abstracted to happen right before the Point Defense fire.