Hey there Mek,
Just wanted to confirm the same problem here. Have upgraded node to latest, reconfigured project, and added nightwatch library as framework type "node_modules" but I only get autocomplete for some things (i.e. waitForConditionTimeout is found, and when using CTRL+B to goto definition, it correctly goes to the nightwatch def. however waitForElementVisible cannot find a definition).
Trying to make progress, lets share our progress if we make any.