I think I found a way
1. Select Node to be removed
2. "Break path at selected node" in the toolbar
3. There are now two nodes at that location. Delete them.
4. Select the two new endnodes
5. "Join selected endnodes with new path" in toolbar
There's no way to do this with keyboard shortcuts, and it should definitely be easier.
@Artha Inkscapes secret tag line is: where there's a will, there's a preference. Probably.
I actually get annoyed by the same auto shape option myself.
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