Right before you posted
I believe there's a registry key for that.
I started hacking the registry...
Here is my findings...
Registry value for MEP...
[HKEY_CURRENT_USER\Software\Autodesk\AutoCAD\R17.1\ACAD-6001:409\AEC\5.5\AecbBldSrv55\Preferences] "HideAecbWarningFlags" and set the key to 2
Registry value for C3D (I am making an assumption on this part, since I havent found a drawing with civil 3d objects to completely test...)
[HKEY_CURRENT_USER\Software\Autodesk\AutoCAD\R17.1\ACAD-6001:409\AEC\5.5\AeccvBase50\Preferences] "HideAeccvWarningFlags" and set the key to 2
Now I need to integrate this into the code, which shouldn't be too hard.