Well, you might want to be careful how far you go with this. I had this same reaction when I first loaded up SH4 - the smoke seemed pretty anemic - but after some research I began to think maybe it was pretty spot on, at least as to the more modern warship/naval auxilliaries at normal steaming speeds - see thread here for a discussion of this issue and some photos and screen shots:
http://www.subsim.com/radioroom/showthread.php?t=110821
I suspect that more/darker smoke would be seen at flank speeds or with older merchants in particular, but I haven't seen any of those things in game yet (just doing sub school practice and bug-hunting so far) so I don't know how the game handles those.