I'm not sure how this works post 4e and the death of a lot of the uber-NPCs due to the 100 year jump and Spellplague, but I've always viewed the powerful wizards of the Realms as basically being in a Cold War; If Elminster can show up and destroy Tiamat's cult in a spell, why can't Manshoon show up in Neverwinter and lay it to waste? For the most part, a lot of the time the uber-NPCs have is spent subtly checking the other uber NPCs. Elminster sends a group of heroes (that the Zhents, Red Wizards, or Church of Bane have no reason to be scrying on) to go do things because if he did them, he'd leave himself too open to an attack by someone wanting to take him down. So even if Elminster went and destroyed Tiamat's cult; he'd be spent on magic and resources and all it'd take is Manshoon to scry on and teleport in fully prepped and finish Elminster off.
If you think of it in the context of the USA/USSR Superpowers, it makes a lot of sense. Both nations had enough nuclear weapons to destroy the other, and they knew any real move against the other would insure Mutually Assured Destruction. So they acted through proxy nations and allies that were much smaller and less threatening in an attempt to gain the slightest advantage. The epic-level mages are the superpowers and they know using their best weapons will trigger others to use theirs (creating a Realms equivalent MAD) so they act through smaller proxy groups (red wizards, harpers, or random adventuring parties) to gain slight advantage.