I found a lot of contadictry info on this myself with reports of one and two scopes but found these which seem to point to the latter of 2 scopes.
Here's a Pic of U-1 the first Type IIa to be launched, appears to have 2 scopes.
http://www.uboataces.com/boa-prelude.shtml
Also a set of plans for Type II German Pre WWII submarine, 1935 (D)
The scope positions seem to match the positions of the U-1 Pic above.
EDIT: Reaper I removed the image because it was very big and could result in long load times for some users. There is a link anyway below to where it can be found - Hitman
Plans found here, also more sets available:
http://www.heiszwolf.com/subs/plans/