There's a custom column that I needed to add to an SCA web store but it should be displayed within NetSuite under non-webstore context...however, when I check the "Hidden" checkbox next to the "Store item" checkbox, it will still show as long as it has display type set to "Normal" and not hidden. I found that I can hide it by checking off "Show only items listed in: item options and custom transaction column fields" under Shopping Catalog > Item Options in the SC configuration. Is there another way to hide custom columns in SC/SCA?

If you mean literally not show it to the customer then you can remove the child view with removeChildView() or even just jQuery.remove()

Thanks, yeah exactly...didn't think of utilizing jQuery for it

Depending on what you are using it for, you may prefer to use display: none instead. For example, some people use custom transaction fields to set values important for internal processes and so need to set the values of those fields. In that case it may easier to write JS that writes a value to that field and then hide it. Deleting it entirely may mess with your data model.