I've run into this problem many times, it's nothing major, adjusting my view or reselecting with lasso instead of shift+clicking the individual point tends to fix it. But it's a little frustrating there's no solution and it keeps interrupting my workflow.
Red circle = un-selectable vertex
As shown in the image, when a vertex is selected the axis (for transforming) displays over it. The issue is that it sometimes is in the way of a vertex and prevents selecting the individual point with shift+click. Is there some way I can prevent this from happening? If I had any idea how to set it up so that holding shift would hide the axis I would give that a try, but I don't. Is there an alternative to context-toggle I could use so that it hides only when shift is pressed?
[Blender 2.79]
The duplicate and answers provided so far do not address what I'm looking for. Seeking to reduce clicks and annoyance, trying to avoid having to zoom in / manipulate view to get a better angle, the toggle would be annoying unless it was only invisible while shift is held.