Also note as per Corbomite's question earlier this thread, that the CE Patch enables hotkeys:
-Fire Pseudo Plasma, Toggle Marine Raids, Convert Shuttles, Select All Weapons.
These are not enabled in OP, and are currently only a CE feature. I'm pretty stupid when it comes to this kind of stuff, but if I understand correctly, someone using a hex editor, might be able to in brute force fashion EVENTUALLY figure out how to enable these hotkeys in OP.
The game uses a so-called map to assign hotkeys to actions. Using IDA, you might see something like "Engage Cloak" followed by an action code of, let's say, 13 01. If I overwrite the action code with, let's say, the one from Emergency Deceleration then my ship will come to a screeching halt when I press the cloak hotkey. Yes, this isn't very useful.
However, there are
unassigned actions, such as Fire Pseudoes, Toggle Marine Raids, etc. Their action codes (18 01, 19 01, etc.) can be used in place of less useful hotkeys, such as Yellow Alert, Self-Destruct, Orbit Target, etc.
The process is a bit more complicated because the hotkey menu will overwrite your custom data every session. To overcome this annoying problem, you have to edit the default map which is nearby. And finally, it helps to update (via aaStrings.txt) the labels on the hotkey menu for your custom assignments...so "Yellow Alert" is replaced with "Fire Psuedo Torps" or whatever.