Besides the obvious benefits of freeing up space for other games or various files you may need, clearing out the clutter of unused game files can also help prevent file conflicts and other issues if you choose to reinstall the game later. It is rare, but on occasion, a fresh install of a game will come with updated versions of the same files you already have, which can complicate installation and lead to crashes or other performance issues.
Removing the files ahead of time not only circumvents the risk of these conflicts occurring, but it is also just a healthy practice to do a full fresh installation if you choose to reinstall the game again. On top of that, it can also make modding a little less of a hassle down the line, since it is often recommended to only mod games you have freshly installed with no extra files.