I recently changed to Inkscape and I think its awesome. But I'm a bit comfused about one thing:

In Illustrator I used to make a hole in a Ellipse (Circle) by adding more nodes / vertexes in the path and deleting one of them.

When I do this in Inkscape the node is deleted but there's no hole. The section just becomes flat.

Any Suggestions?

I'm not familiar with Illustrator, but can hopefully answer your questions.
By "hole in the Ellipse", do you mean like removing a pie wedge? Or do you mean like a...washer, the kind you put on a bolt? If you're looking for the pie wedge thing, check the tool control bar (across top of canvas). You'll see an icon to make arcs and one the pie wedge thing. Drag the tiny circle to open up the wedge.

If it's like the washer, you'll need to make a large circle and a smaller circle, the size you want the hole to be. Then use Path menu > Difference.

Also, please see the info in my signature for some great instructional material.