Some musings on the minor flaws in NCC-1701, no bloody A, No bloody B, C, or D. And some reasons why you didn't want to be a redshirt on board either...
Regarding the Self-Destruct talking loud, the designers probably didn't envision it being used in a scenario where a handful of officers had stolen the ship and were able to flee without the enemy knowing. The thought was probably that the benefit of informing a friendly was worth more than the risk of tipping off an intruder. Also, the self-destruct might actually scare and throw off an intruder in a beneficial way.
No, in the 365 book (which detailed every episode) they calculated something like 24 people died in the series, and 70% had red shirts, hence the label. A lot of people miss the meaning of "being a red shirt" and what it implies. It was nothing intentional, Gene Roddenberry felt that the security teams would naturally have the higher rates, but using different writers for each episode kinda allowed a field day on the poor guys.
Regarding the Self-Destruct talking loud, the designers probably didn't envision it being used in a scenario where a handful of officers had stolen the ship and were able to flee without the enemy knowing. The thought was probably that the benefit of informing a friendly was worth more than the risk of tipping off an intruder. Also, the self-destruct might actually scare and throw off an intruder in a beneficial way.