Hi,
d3d9.dll is the main DirectX 9 dll (Direct3D).
It should not exist normally on Skyrim main folder (and it's added - modified - by some 3rd party fixers, tools and mods in order to override the normal one).
DirectX 9 is installed with a separate installer exe, shipped with the game, and all of its file will be put in the normal windows/system32 folder.
If d3d9.dll is placed in root skyrim folder, it could override the system32 one (according to how the tesv.exe behaves).
The game however is designed to work with a specific dll, which is part of the normal directx installation.
If you change this behaviour, everything depends on
what that new d3d9.dll contains and how it has been made/modified...
The normal main folder of skyrim should contain only following dlls (for 1.3 patched version):
-atimgpud.dll
-binkw32.dll
-steam_api.dll