I decided to test this. Two target ship classes with 25 layers of armor, one mounted with a point-defense laser and the other with a CIWS system.
The missiles I built used 8x warhead per MSP and extreme x-ray laser head tech. The standard warhead missile was 2msp for 16 warhead. Interestingly, the number of laser heads is determined as Size in MSP (2MSP, 2 heads), and the option increased total damage by 25% (From 16 to 20, from 4 to 5, from 12 to 15). Damage per head is total damage / number of heads, so 2 heads with a total damage of 20 means each head does 10 damage.
Finally, as to the tests. Standard missile did the expected footprint, locked up by point defenses and CIWS. Laser heads, on the other hand, bypassed final defensive fire completely. Interestingly though I found that they use the missile damage footprint rather than the laser damage footprint -- I had a nice 10-damage 3-deep crater with the extra point of damage hanging off.