When you add and remove data to the sqlite database, it grows but never shrinks. Think of it like a river that rises and falls, but the water line always remains. This waterline is the space used on your hard drive.
To reduce the footprint of the database, you can run the VACUUM command to shrink the data base.
import sqlite3
import arcpy
SQLITE_FILE = r"c:\temp\example.gpkg"
conn = sqlite3.connect(SQLITE_FILE)
conn.execute("VACUUM")
conn.close()
Pretty simple to reduce the size of the database. What VACUUM does is reconstruct the database from scratch. This will leave the database with an empty free-list and a file that is minimal in size. Note, however, that the VACUUM can take some time to run and it can use up to twice as much temporary disk space as the original file while it is running.
Enjoy
