Identity signals can be spoofed and friendlies can suffer damage to identity signaling systems. If a commander had to choose between giving the enemy the chance to disable their weapons, or trust in their forces to not shoot each other or walk into the line of fire and just accept some occasional friendly fire losses, they'd choose the second option every time.
It'd make a lot of sense for intelligent munitions to electronically shield itself and no longer accept signaling after being fully armed and fired to prevent counter-measures from interfering with its mission, or even worse, being used by the enemy. Intelligent munitions and everything they involve are also a lot more costly to produce.
I'm not an industry expert on the matter but as far as I know, Identity signaling just gives weapon controllers a message of who they're aiming at, and it's the weapon controllers' perogative to shoot or not.
To answer your question, my take on friendly fire is that FF is an integral part of warfare. Removing FF completely changes the way war is waged. It's typically instituted because the idea behind the game is completely untennable with FF, whether through game functionality or multiplayer griefing. Logic and historical continuity need not apply to fictional works.
Either way, the ACTUAL problem you're having an issue with is either AI deficiencies or you're just blindly moving into the path of oncoming weapons.