That is an interesting question. I would guess they smoked a lot of Turkish or Oriental blends since they would have had more access to it after the war started. They may have also smoked some latakia heavy blends since it would have been available to them.
I've seen a number of historical photos showing enlisted men in the German army smoking pipes also so I don't think it was just officers.
Someone else will correct me if I'm wrong but I don't believe there were as many aromatic blends in existence back in the 1930s & 40s. My impression is that the explosion of aromatic flavored tobacco didn't happen until after the 1970s.
Aromatic mixtures were well established way before the '70s. I was born in 1950 and started smoking a pipe when I was a young teen, back in '66. The vast OTC selections were mostly aromatics....Mixture No. 79, Amphora, Walnut, Revelation, Velvet, Prince Albert, etc. I'll bet many of these old blends were already known, popular, then smoked during WW-2, and were still popular when the soldiers returned home. My dad was in the Coast Guard and he smoked Mixture No. 79 when he was stationed in Alaska, so these old aros were popular and sold way before WW-2.
It would be an interesting project to search through vintage magazines for old pipe-tobacco ads, especially German magazines printed in the 1930s...and later. I would imagine that the friends and relatives of soldiers must have sent them some cigarettes, pipe-tobaccos, along with the necessities, essential items, and goodies from home.