You're right, and it can make writing adventures very difficult. One of the causes for so many high level NPC's, I believe, is the assumption by Wizards of the Coast that there are many groups playing at high level. A lot hand out experience and treasure very fast, also, and want a high-powered, high magic game. The books may be loaded with high level NPC's, and so many with unique powers like Mystra's Chosen, because they're there to balance the scales and to help DM's keep players a little humble. Most groups probably come at this problem at low or medium levels, but from the point of view of a group where everyone is at least 15th level, let's say, and for some higher than this, the power gap is smaller and the PC's relative share of responsibility to tackle the biggest problems facing the setting is bigger.
A lot of Forgotten Realms players may want a very epic game. I can remember an old Forgotten Realms book about the City of Raven's Bluff, published with input from the RPGA Network and its Living Realms campaigns, where the owner of a magic item shop was a 40th level magic-user. For the same rules system, that was eleven levels higher than what was printed for Elminster, and ten levels higher than for the Simbul. And that was just a shopkeeper, a retired adventurer. I don't think they had invented the extra abilities for Elminster and the Chosen, either.
Going back further, there was a super module set in the Forgotten Realms, called H1-4: Throne of Bloodstone, I think, and the pre-generated PC's were set at 100th level.