I don't have such black lines with any configurations, DirectX or OpenGL, windowed mode or full screen, low resolution or high resolution, antialiasing or not.
The plugin does not resize them to size of power of two. Textures in DirectX or Opengl are always created as size of powers of 2, and images are loaded into the top-left corner of the created textures. If the size of a texture image is not powers of 2, it won't fit the whole created texture in DX or OGL, and remain part of the created texture will be in black (in fact, could be random data since the memory is not cleared to 0). In such a case, different setting for the texture, such as filter type, texture repeat setting, could cause the black lines.
Suggestion:
1. Don't use high-res texture, to see if you have the black lines
2. Use hq4x filter without high-res textures, to see if you get the black lines
3. Check your setting in the "Texture filters", make sure let the option "Force texture filters" to the value "N64 default texture filter"