The trash is not emptied automatically in GoodNotes. To empty it, tap the Gear icon in the top-right corner of the Library view > Trash Bin, and tap on "Empty" in the upper right. Note that this is permanent and deleted items cannot be recovered anymore.
Also, if the Trash Bin has a lot of items, emptying it will take a while, so please wait for it to finish even if it seems nothing is happening.