WELCOME ABOARD!
My PC won't let me play SH4, but it's the same with all of them: As breadcatcher said, take your time, practice with the single missions until you feel comfortable with the more difficult parts, don't let that stop you from playing careers on the easier levels, and keep posting here, even if it's drivel. We'd rather talk to new folks than not. You'll find all the advice and help here you can think to ask for, and given freely and cheerfully.
1) Destroyers may spot your scope at any time, but the longer you leave it up the better the chance you'll be discovered. Silent running during your attack can cause problems. Just keeping the speed low will help if they aren't already looking for you, and if you forget to disengage it your crew won't load torpedoes or do repairs.
2) Yep, sounds like the way to do it to me. Work into it at your own pace. The hardest realism move is the final step of turning off the external views. It's not losing the knowledge of everything going on - that's actually better when you don't know - but the loss of the beautiful close-ups and screenshots that's hard.
3) That's SH4-specific, so someone else will have to fill you in on that.
As for becoming more skilled, just remember that the real skippers had months of intense training and years as subordinates to develop their skills and learn from the ones who'd already been there, so we're at a disadvantage. On the other hand, we can learn from our mistakes - even the deadly ones, which gives us an advantage they could never have.
Good hunting!