Where does Windows store icon positions?

They are located in the registry under HKCU\Software\Microsoft\Windows\Shell\Bags\1\Desktop.

The key that should interest you is the ItemPosXXXxXXX(where XXX is your resolution).

The relevant values are Mode, LogicalViewMode, IconSize.

You can combine them as shown in the table:

Style       Mode    LogicalViewMode  IconSize
X-Lg Icons  5       3                0x100
Lg Icons    5       3                0x60
Med Icons   5       3                0x30
Sm Icons    2       3                0x10
List        3       3                0x10
Details     4       1                0x10
Tiles       6       2                0x30

Update

Fortunately found an article that can help you. See: Windows Shellbag Forensics.