First let me start by saying, I don't have enough pictures with orientation flags to test if that is always the case. However, it was always the case for me and these documents agree that orientation is in the first IFD:

http://www.sno.phy.queensu.ca/~phil/exiftool/TagNames/EXIF.html
http://www.media.mit.edu/pia/Research/deepview/exif.html