I want to connect two nodes which are already at the same spot:
Here you can see it's actually 2 nodes:
I need to select them both as they are (atop of each other) and join them. This is the desired result:
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There are two easy ways:
Drag a selection rectangle over the position.
Make use of the fact that Inkscape preserves selection when you undo or redo actions: Move one node away, select both nodes and then undo.
For some reason, if you select two nodes at the same position, they are not rendered anymore. Nonetheless, if you hit join selected nodes, you get the desired result.