You can use sqlite3_analyzer from https://www.sqlite.org/download.html.
It’s a really cool tool. It shows you the number of pages used by each table with and without indexes (each page, by default, is 1024 bytes).
This is a sample sqlite3_analyzer output for the Northwind database:
*** Page counts for all tables with their indices ********************
EMPLOYEES............................. 200 34.4%
ORDERS................................ 152 26.2%
CATEGORIES............................ 90 15.5%
ORDER DETAILS......................... 81 13.9%
CUSTOMERS............................. 17 2.9%
SQLITE_MASTER......................... 11 1.9%
PRODUCTS.............................. 7 1.2%
SUPPLIERS............................. 7 1.2%
TERRITORIES........................... 6 1.0%
CUSTOMERCUSTOMERDEMO.................. 2 0.34%
CUSTOMERDEMOGRAPHICS.................. 2 0.34%
EMPLOYEETERRITORIES................... 2 0.34%
REGION................................ 2 0.34%
SHIPPERS.............................. 2 0.34%
It also generates SQL statements which can be used to create a database with usage statistics, which you can then analyze.