I am quite quite puzzled about how hiding datasets is intended to work when editing a workflow.
When editing a workflow, on the output of any tool (in the main part of the screen) next to the grab point for linking tools there is a "snowflake". This is either greyed out (which means hide the output when the tool is run) or yellow (which means the output is kept in the user's history), and you click on it to toggle this.
Additionally, on the right hand side in the "Edit Step Actions" there can be a "Hide Dataset" action.
My impression is the two UI mechanisms are intended to control the same thing - but toggling one does not affect the out (at least, not directly).
For example, toggling the "snowflake" does seem to alter the right hand side (add/remove the "Hide Dataset"), but only after you save, close, and reload the workflow.
Is this a bug? If so, the simplest way to solve this (from a UI perspective) might be to remove the "Hide Dataset" action from the right hand side.
On a related point, if I extract a workflow from my history, all the steps have their "snowflakes" greyed out - even the final step in the history. Yet despite this, when I run the new workflow all the output is kept (nothing is hidden).
After a little experimenting, my guess is that you have a special case: if all the outputs have greyed out snowflakes, rather than running the tools and hidding all the output, you hide nothing.
I would expect a new workflow extracted from the history to have all the output kept (yellow snowflakes), or perhaps intermediate output hidden (greyed out snowflakes) with the output from the final history step shown (yellow).