Inn 1939-40 they had the biggest airforce in the world but that was changing quickly
They only do 4 kts underwater if you know where they are they arent a problem, coming anywhere near the surface leaves them open to being rammed or depth charged. A completely different situation to the open Atlantic.
Like I said, if the U-boats are screening the invasion force, the RN options for attacking them are very limited. Thus the submerged speed isn't nearly so critical. Also the Type VII A&B (what they had at the time) had a top submerged speed of 8 knots. They could cruise for a couple of days at 4 knots. I don't remember how long they could maintain 8 knots. It would have been over two hours, but they wouldn't want to push it for much longer than that.
You are correct about the size of their airforce, but at the time of the invasion of France the Germans had 850 109's to the rest of the Allied forces 800, so not a huge advantage. The main advantage the Germans had was they were dictating the actions. The Allies were reacting, and usually not very well. It wasn't until the retreat to the UK, and their radar, that the British gained the predictive ability to react well.