First, WELCOME ABOARD!
Now, in answer to your question. The original (and to some, still the best) u-boat sub sim, Aces of the Deep, was exactly like what is in SH3 today; that is, you go out, sink ships and come home again. The original Silent Hunter was very similar, though sometimes you would recieve a radio message ordering you to do a photo recon or lifeguarding mission. There was no extra reward for those, and no penalty if you didn't do them. I don't think anybody ever complained about those, but it was a little before my internet time, so I don't know for sure.
In Silent Hunter 2 you had mission assignments, and nothing else. No real career, and each mission was much like a first-person shooter: fail to complete the mission parameters, or die, and you repeated the mission over. Everybody liked the game, but hated that part.
Now for Silent Hunter 3. When it was still in production they announced that their 'campaign' would be a modified form of SH2's, though much more advanced. Pretty much everybody protested, and after several weeks of polls they announced that after a 6-month delay, SH3 would have a dynamic career mode "just like AOD's". SH4 has been an improvement, with specific missions mixed in, but that is why SH3 is the way it is. It's hardcoded that way, and it can't be changed or 'fixed'. Sorry.
Me, I play it because I like submarines and want to re-create the feel of being there. Patrolling an empty grid doesn't bother me at all. I even waste whole gaming sessions sailing in and out of my home port looking at all the cool stuff.
But that's just me.