It's essentially because HGSS is a Gen IV remake of a Gen II game, and therefore part of Gen IV while being set in Johto & Kanto.
When the number of Pokemon in the National Dex have expanded, it's kinda assumed in the Pokemon universe that the previous regions that Ash has explored also become aware of these newly discovered Pokemon. Johto doesn't continually have 256 Pokemon in its National Dex, otherwise it'd be in the dark ages compared to the 649 Pokemon known in Unova. Of course the games themselves don't update, but it's assumed in the universe that the Pokemon newly found are made known to everyone.
From a marketing standpoint, it'd be really pointless to buy HGSS if it had the same Pokemon GSC had, when DPPt had a truckload of new Pokemon plus most of those in HGSS.