Try importing a named range instead.
That would solve the problem on import but once the spreadsheet is updated (which is the point of the tables being linked) the empty cells reappear.
The default range of cells in the import options includes the empty cells, so it's as if InDesign thinks there is information in them that should be imported.
From my previous experiences you may help indesign by applying a stroke onto your excel table (I mean doing it inside excel). Ensure no extra contents are located in surrounding cells like spaces for example.
But it's likely you won't get a way to get updates free of issues. Have you ever considered EasyCatalog ? It's a terrific tool for makings structured layout such as catalogs and especially tables.
Adding a stroke didn't work
EasyCatalog looks great but that would be a more long term solution.
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The answer was actually very simple. Just delete the offending column or row in Excel.
If an empty cell has left, centre or right alignment formatting regardless of whether there is data inside InDesign will interpret that as a cell that needs to be imported. By default a cell should not have any left, right or centre alignment. Removing the column or row fixes the issue.
Wish I'd discovered this earlier! Thanks everyone for trying to help.