I'm going to take a guess that "special weapons" means things like phaser lance, phaser/disruptor/plasma lotus, etc. Those don't fire off because the game treats them as skills and not as weapons. If that wasn't what you meant, my bad. It's a bit hard to tell what you mean.
Because they are consoles, and not weapons (for the game). Also, they usually have a much longer cooldown than any other weapon (2m for most of them), and they don't want players complaining because they activated a special ability on an almost dead target.
You can still bind your special abilities to spacebar, if it's what you want.
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Mine Trap Supporter
You can still bind your special abilities to spacebar, if it's what you want.