While you are correct that the angle would be ever slightly different from the periscope to the bow of the boat I wouldn't go as far as 3-4 degrees. In fact you can see for yourself. When you have a target in the scope see what the angle of it is from the periscope then clammer on down to the bow of the ship and use your binoculars to see what the angle is there.
For your question about angling a torpedo I had this issue for a while, but the short version is that the torpedo control from UZO or the periscope is calibrated to work from there for a reason, so you don't have to worry about the discrepancies.
You can use various tools like the attack disc to determine the 90 degree intercept course for the best shot. Remember that the angle on bow changes depending on the target positon, it's impossible to keep it at 90 unless you were drifting sideways along the target course while facing it
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