If you have 2 copies of the same file, it will only count 1x towards your storage quota. This makes quite a difference for two reasons.
First, we keep a version history of your website. Typically, there is only a minor difference between versions. So if you have 100MB of images, and 100 versions of your website, your images still only consume 100MB of space, instead of 10000MB. Big difference.
Second, you will install packages to extend the capabilities of your website. These packages will easily take up 1-2GB of uncompressed size, while only take up maybe 100MB compressed. (For techies: that's because packages form a dependency tree, often having some base packages installed several times.)