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I believe the fields set to hidden or those conditionally hidden will not be displayed in the Form Designer Tool. Here's an example test form I made:
Here you can see I have an address field that is set by default to hidden.
In the form designer tool, it won't show up.
Same cases for those fields that are conditionally hidden.
I believe this is somewhat a bug or a design flaw. The fields displayed in the Form builder should also be displayed in the Form Designer Tool to further design the hidden fields without requiring them to be unhidden.
I will forward this to our developers to have it checked. Apologies for the inconvenience. For the meantime, you might need to disable or un-hide them first if you are designing them in the Form Designer Tool.
Apologies for the inconvenience.