The amount of space that a group of missiles take up on a ship is different than all the other components on a ship. The missile launchers themselves are considered to take up space. That means that instead of just taking up the rack space number, they take up (RS + 1). So if you use the default 5 racks, the actual space the missiles take up is equivalent to 6 racks.
A common strategy in MoO3 is to use the 'Shoot and scoot' tactic. This involves loading up a ship with 1 rack of missiles, and packing in as many as will fit. Note, the actual size that is used is (1 + 1), or 2. The ships will then attack an enemy position, shoot all their missiles, and then retreat, often before the enemy can attack them.
This patch is designed to weaken the effectiveness of that tactic (as the AI can't compensate for it). It changes the '+ 1' from (RS + 1) to '+ X', where the X is whatever number you prefer.
NOTE: This patch is superceded by the Autobuild patch. They are not incompatible (ie, you may have both installed without creating conflicts), but if the Autobuild patch is installed, this one will not function.