Lines appear transparent when below a certain thickness

Photoshop, like any other raster image editor, works in pixels. So a pixel is the minimum unit available in your image. There are no half pixels in a raster image, only whole pixels. If you select a line width of 0.5 pixels then the only way to display that using whole pixels is to reduce the value in that pixel, or make it transparent, which is what you are seeing.

Dave