My XBAP application uses two win32 dlls and as usual many .Net dlls. Since we add .net references to the project itself, that is not a problem, as they all get deployed auto
Can you try:
Checking your project properties under the Publish > Application Files section and if your native dlls appear there, making sure they are set to include.
Try including the dlls as content files in your project with copy to output directory set to Copy Always (I would think this may make them appear in the list of references mentioned in point 1, allowing you to set them to "Include").