The version of sqlite you get when you do import sqlite3 in python is is determined by the version of libsqlite3 installed on your system, not the version of the binary.

To check what version of sqlite you are using you can check the sqlite_version string like this

user@penguin$ python3
Python 3.5.3 (default, Sep 27 2018, 17:25:39) 
[GCC 6.3.0 20170516] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import sqlite3
>>> sqlite3.sqlite_version
'3.16.2'
>>>

To upgrade to a more recent version in Debian Stretch it may be necessary to get the package from backports.

echo "deb http://deb.debian.org/debian stretch-backports main" | sudo tee -a /etc/apt/sources.list
sudo apt-get update
sudo apt-get -t stretch-backports install "libsqlite3-dev"