Yeah, two directories are still needed, but as you said you can hide corrupted icons:
Go to recovery menu (hold R at startup) -> Configuration -> "Hide corrupt icons".
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C2D E8400 3.00 Ghz | EP45-DS3 | HD4850 512MB | 4GB DDR2 800 | 640 + 250 GB HDD
SyncMaster 2233BW 22" | Logitech G5 | Logitech G15 | Windows 7 x64