With little activity I decided to find out myself; I'm taking my submarine on a round the world trip!
The point of the whole is to find out wether or not the geographical and meteorological patterns change.
I didn't pay any real attention to the Atlantic – for obvious reasons. Though I did notice that the further south I got, the water got a brownish kind of color.
Route:

I don't want to make it all too picture heavy, but so far I've discovered changes in botanical organisms – there are palm trees in north-eastern Brazil.
Weather across the Atlantic was as expected – cloudy. However, I did not encounter any storms while travelling through the
ITCZ.
When I get to the Pacific I'll start gather data on weather patterns and see if I can come up with something.
You know, there's probably an easier way of finding this out to be honest. I'm just failing to see it.
One thing that didn't escape me though; why did Allied merchants move close to the Brazilian coast? All the ports in the area are neutral (with the harbor mod), there are two in the middle of the Atlantic, however these merchants were travelling south, towards Brazil.
They are scripted to follow certain routes, right?
On my trip back to Germany I was planning on going through northern Canada; is this even possible or would I have to run at minimum speed while submerged to get out of there alive?
Der Kampf geht weiter!