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Digging deeper with the Visual Studio debugger, I discovered the following interesting outcome (run with cmd.exe):
 @echo off
 mklink /d sample sample-target
 mkdir sample-target
 echo "" > sample-target\__init__.py
 :: Before KB2467174, returns 0; after, returns -1
 python -c "import ctypes; buf = (ctypes.c_char*256)(); print(ctypes.windll.msvcr90._wstat64i32(u'sample', ctypes.byref(buf)))"
 :: Always returns 13
 python -c "import ctypes; fd = ctypes.c_int(-1); print(ctypes.windll.msvcrt._wsopen_s(ctypes.byref(fd), u'sample', 0, 0x40, 0))"
 rmdir sample
 rmdir /s /q sample-target
The call to _wstat64i32 is returning -1 with the patched CRT... but when I traced _wstat64i32 (on a machine with the patched CRT), it called _wsopen_s, which apparently always returns -1.
So my guess is that the patched CRT changed something about _wstat64i32 such that it doesn't defer to _wsopen_s. I'm going to see if I can get an early version of Visual Studio that I can trace where _wstat64i32 doesn't fail.