Okay I'll try and answer this :)
If your on about this waterfall where Lugia appears from when summoned.
You cannot use HM Waterfall to go up this waterfall because it is not an accessible area in the game. As you can see it is surrounding by rocks blocking the player from attempting to go up the waterfall.
The purpose of the Whirl Island's was to be the location where you can capture Lugia in your game. It plays a huge part in SoulSilver but a slightly lesser part in HeartGold since it is not part of the main story in HeartGold. After you capture/ defeat Lugia there isn't another purpose of the Whirl Island's.
Game Freak probably just made it so you couldn't go up the waterfall because normally if you see a waterfall in the games and you can go up it there's normally an item such as a TM up there. But because in SoulSilver and HeartGold there are two regions combined into one game, items and TM's had to be considered carefully where they were all going to be put. I think another reason might be because the waterfall is just to increase Lugia's appeal and is just part of decoration in the room.
This is an image of the top of the waterfall from a distance:
For the main reason why they didn't let the player go up the waterfall you would have to ask Game Freak directly but it was probably to do with what I've said above.
Hope I helped :)