Sober, what do you mean by indicator loops? Also, what are those boom defenses? Are they the wrecks blockades? Sadly, we cannot recreate all that stuff as for now we have only mines and nets, but I think that should be enough to stop the free fun in Scapa.
Anyway, Scapa is completely reworked now but the new defences will be available after Prien historical attack date, So there is a short opportunity for everybody to be Prien, after October 39 Scapa is sealed. And even if someone will manage to get through somehow, it will be almost impossible to launch torpedoes as they will never hit any target. At least in theory.. who knows, maybe we have another Prien among us.
Regarding the mines... the stock campaign out of box is a joke. Go there, sink that, show off on u-play

This is a sim about WW2 and a warmachine and doing damage to the enemy is not going to be unpunished. Only skilled captains should survive and be awarded on returning home. If.. is any return home.
But this will not be a mission impossible. You got you mine map and the mines itself will not be a 1 shot kill, but your sub will be disabled for a long time. So you will need to plan careful your route. Or.. take you chances and try to force the mine blockade, raid ports etc. Everything has a cost, there is nothing free.
And for those who play with high realism and real nav, this will be a really hardcore experience :P