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It depends on the layer type, and the two rules are opposites. A hidden text layer is kept as a fillable slot. A hidden smart object is not exposed at all.

A hidden smart object is not a slot

A smart object hidden in Photoshop does not appear in the upload response and cannot be addressed. Make the layer visible in Photoshop and upload the file again. The upload tells you when a file contains one, so you know which layers to turn on before re-uploading.
Sending a UUID you copied from somewhere else for a layer that is not in the response returns an error rather than rendering it.

A hidden text layer is a slot

A text layer hidden in Photoshop stays in your template as a fillable slot. It renders only when you send wording for it, and stays hidden when you do not.
Leave the entry out and that line does not appear. Nothing in your source file is changed either way.
This is how one template carries optional lines, personalised fields and language variants that appear only on the renders you fill. Design the alternatives once, hide them, and switch each on per render.

Check what a template actually exposes

A smart object you expected and cannot see in that list is hidden in the PSD. Turn it on and upload again.
Use that against an existing template rather than re-uploading it, since every upload creates a new template.

If the layer is listed but still renders unchanged

That is a different problem. Check the response for TEXT_OVERRIDE_NOT_APPLIED or TEXT_LAYER_NOT_EDITABLE: both mean the layer was found and kept its original appearance, and the support matrix on Text layers says which limit you hit.

PSD compatibility

Hidden layers alongside every other feature rule.

Text layers

The override contract and the warning codes.