No the engine upgrade is not really a cheat, though, I suppose that depends entirely on what mod you are playing. If you are playing GWX my sister basically explained to me that the upgrades only provide a slight performance increase, as compared to stock where a MAN VIIC could do 20 knots on a calm sea which is very unrealistic.
The anti-sonar and radar coatings, I don't actually use them. They were not widely available and were only used on a few boats, so I "slum it" like all the other U-boat captains and don't use it. Of course, I dare say life would be easier for me if I did use it, but, heh - I is a glutten for punishment!
As for GWX depriving you of your surface cruising, not true. You can run on the surface but in late war you are going to get caught by planes a lot. Also one tip, don't bother getting a snorkel on your sub until the snorkel sensors are available.