However as a best practice usually you have dedicated sheet (visible only for NPrinting user) with copies of objects you utilize in NPrinting reporting. This then is not visible for end users and it is not so much annoying anymore.
My best practice though is to have dedicated for NPrinting reporting QlikView application. This is usually loaded only with fields and objects i need for reporting which then works usually much faster and is easier to work with. This also is not affecting my application used by users. I know it is "double work" as you need to maintain 2 applications but from performance point of view is much better solution. I usually use binary load or full optimized QVD load to feed source to NPrinting QlikView App
I also experienced this (NP 17.5) but it was not due to hidden columns in my chart. In my case, it turned out to be that when I changed the order of the columns in my chart, republished it to Access Point, reloaded the metadata in NP, and then updated my chart in the NP report designer, it didn't render the column order correctly. I had to remove the chart from the Tables node in NP designer and re-add it, and also remove and re-add the columns to the excel layout.