As mentioned above, the "D" in "OD" follows from its ring orientation pattern being the same as that of 2C-D (and this, originally from the mimicking of the pattern of DOM). All of these D- compounds have the 2,5-dimethoxy-4-methyl ring-substitution pattern.
PiHKAL # 14 BOD
Still never made any sense to me. DOM has the 2,5 dimethoxy 4-methyl substitution, but the "D" in the name as posted above is for desoxy, and the "M" is for the Methyl group, to separate it from DOI, DOC, DOB, etc.
I don't understand why he chose 2C-D and not follow the the naming scheme and use 2C-M? A methoxy on the 4 position would make 2,4,5 tri-methoxy phenethylamine, and wouldn't fall under the "2C" naming scheme, and in fact is named TMPEA in Pihkal. Instead we have tons of non-"D" with a 2,4,5 substitution pattern, such as Ariadne, 2C-D, BOD, BOHD, etc etc in the book. If you discount the 2,4,5 but keep the methyl in the 4 position there's a ton more as well.
Maybe it was just too damned hard to make up a fully logical naming pattern so he just said fuck it, chemicals with a methyl group in the 4 position will be named whatever the hell I want them to be named
