During initial testing, a very large volume of damage beams has been found to do vastly lower SHP damage to entities than cannons removing the same numbers of blocks.
I suspect that damage beams do not remove SHP from a ship's SHP pool when blocks are destroyed by beam penetration - only the initial beam impact point seems to count. Meanwhile, this problem does not apply to cannon projectiles, which act as though they are impacting each block for the first time as they pass through an entity's structure.
The beam array in question is a 70920 module Cannon/Beam/Overdrive system with 197 or so outputs.
Image references:
http://i.imgur.com/UbISizD.png
This damage to a 1,000,000 block ship only dealt 6% SHP damage.
http://i.imgur.com/cS8Pc2a.png
This damage to a 1,000,000 block ship dealt 40-50% SHP damage.
The number of blocks removed is very comparable between the two, yet Cannons dealt roughly 9 to 10 times as much SHP damage.
For reference on a 4.5 million block ship, this image displays roughly half of the damage necessary to overheat the ship - more damage of a similar nature is found in the front, rear, and other side of the ship.
http://i.imgur.com/u0YFUMC.png