I'm not sure that I can give you correct answers because I also still don't understand quite well what is going on in game regarding crew related abilities and commands. This needs further testing...Luckily, I have you guys...
I know this though:
Yellow hammer- no function
Silent running- no obvious effect on submarine noise signature but I wonder was there any effect ever, in any SH game?
Torpedo loading stopped, no propaganda to increase moral.
- Doubled SR/ BS commands - that commes from TDW NewUI's, why? I don't know...
This is the thread which deals with mentioned problems, maybe there you can find some answers...
http://www.subsim.com/radioroom/showthread.php?t=195193