How can I clear all my Safari bookmarks on iPad Pro?

Bookmarks can be shared through iCloud to all your Apple devices that have Safari. Then changes on iPad would propagate to other devices. Verify if that is what you intend to do. You can exclude a device, on that device, through Settings﹥[You/​Apple Account]﹥iCloud﹥Save to iCloud: See All﹥Safari﹥Off.

You can group Bookmarks/​Favorites into folders (and sub-folders) for organizational purposes, and limiting how many options are presented at once.

You may edit the Bookmarks on iPadOS from within Safari, then reveal the sidebar, then Bookmarks, then Favorites, then Edit (bottom of the screen in the sidebar). That would present a delete (−) button next to each item. That works on folders of Favorites too.