I think this is a common misconception of Ebberon's world building. There is high level magic, about as much as Krynn, Mystara, or most of Oerth. The two things is that high powered magic is not openly part of society. Magewrights, dragonmarks and dragonshards free high level wizards and clerics from the mundanity of running temples and building lightning rails, so that they can be threats and important allies, not merchants. Or on the other side, not so many of them that the PCs are never not needed. There is no "let Drizzt or Elminster handle it" scenario, you aren't playing the Defenders waiting for the Avengers to show up, but it also doesn't mean Dr Strange and Dormammu aren't there behind the scenes either.
Limiting Eberron to only low level magic/play (e6) robs Eberron of the biggest threats: Daelkyr, Lords of Dust, the Quori, the giants of Xen'drik, the Lord of Blades, Lady Vol, etc. They exist and threaten Eberron in a variety of ways. You need someone to handle those threats and if Eberron doesn't have a Circle of the Eight, it's gotta be your PCs.
I think the other issue is that in D&D, magic item creation was primarily the realm of high level wizards. Eberron didn't want to make every member of house Cannith a 9th level wizard, so they created the cheats needed to allow low level non-wizards to make magic that replicated modern technology. That doesn't mean 9th level wizards don't exist, just you don't need a lot of them to justify the absurd level of everbright lanterns in Sharn.
So yeah, 9th level wizards still exist in Eberron as NPCs, it's just there aren't thousands of them and they aren't spending their days making eternal wands.