Yeah, in Japan, there are several times when the set is really divided into two boosters, but this isn't done internationally, and so HGSS will be combined of both heartgold/soulsilver.
A good example to look at is Diamond and Pearl. Diamond and Pearl were seperate boosters in Japan, but were then combined into one set when it was internationally released so things wouldn't get complicated when the set were to be divided.
So yeah, HGSS will have both of the cards from heartgold and soulsilver. Thus, the two sets are combined into one set yet again, like what's usually done.