In my example below, the mask works as it should on the green and blue lines, but makes the horizontal red line disappear altogether. When the mask is removed, the red line seems to have nothing wrong with it. What's going on?
document.querySelector('button').addEventListener('click', function(){
document.getElementById('problem-line').removeAttribute('mask')
}, false)
<svg width="400" height="180">
<defs>
<g id='circle'>
<circle r="50" cx="100" cy="100" />
</g>
<mask id="hole">
<rect width="100%" height="100%" fill="white" />
<use xlink:href="#circle" />
</mask>
</defs>
<use xlink:href="#circle" opacity='0.5' />
<line id='problem-line' x1='100' y1='100' x2='300' y2='100' stroke='red' mask="url(#hole)" />
<line x1='100' y1='100' x2='300' y2='50' stroke='green' mask="url(#hole)" />
<line x1='100' y1='100' x2='300' y2='150' stroke='blue' mask="url(#hole)" />
</svg>
<div>
<button>Remove mask</button>
</div>
The default for maskUnits is objectBoundingBox. The key issue you have is described in the last paragraph of the specification text.
Why not use a rect with a fill rather than a line with a stroke if you've got a horizontal line? Or alternatively use userSpaceOnUse units.