I seriously doubt that empty folders, even assuming you had a thousand of them, would make much difference in the size of the backup.
If it's drive space that's the concern, either delete an older backup that you no longer need, or buy another drive. Many 1TB HDD's can be had for as little as $59.99, sometimes w/free shipping, just hunt around for bargains, and sign up for promo email from major etailers like Newegg.
Then, all you'll need is a drive enclosure, these can be had for as little as $15 on eBay & Amazon, and even Newegg. It's just that when considering a enclosure, regardless of the source of purchase, read the feedback on it. Amazon & Newegg lists feedback, use Bing or Google to research any purchase you consider making from eBay sellers, and make careful note of the seller's feedback ratings. More than 5 negatives within the last 30 days is a good sign of a dishonest seller.
The reason that I recommend assembling your own, which takes less than 5 minutes, is that you can buy a much higher capacity drive for those pre-assembled ones, and some of those develop defects within the case. I've assembled 2, and both are much faster than the pre-assembled 500GB Seagate that I purchased over a year ago.
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