Suppress warning messages using mysql from within Terminal, but password written in bash script

If your MySQL client/server version is a 5.6.x a way to avoid the WARNING message are using the mysql_config_editor tools:

mysql_config_editor set --login-path=local --host=localhost --user=username --password

Then you can use in your shell script:

mysql --login-path=local  -e "statement"

Instead of:

mysql -u username -p pass -e "statement"

I use something like:

mysql --defaults-extra-file=/path/to/config.cnf

or

mysqldump --defaults-extra-file=/path/to/config.cnf 

Where config.cnf contains:

[client]
user = "whatever"
password = "whatever"
host = "whatever"

This allows you to have multiple config files - for different servers/roles/databases. Using ~/.my.cnf will only allow you to have one set of configuration (although it may be a useful set of defaults).

If you're on a Debian based distro, and running as root, you could skip the above and just use /etc/mysql/debian.cnf to get in ... :

mysql --defaults-extra-file=/etc/mysql/debian.cnf

One method that is convenient (but equally insecure) is to use:

MYSQL_PWD=xxxxxxxx mysql -u root -e "statement"

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Note that the official docs recommend against it.
See 6.1.2.1 End-User Guidelines for Password Security (Mysql Manual for Version 5.6):

Storing your password in the MYSQL_PWD environment variable

This method of specifying your MySQL password must be considered extremely insecure and should not be used. Some versions of ps include an option to display the environment of running processes. On some systems, if you set MYSQL_PWD, your password is exposed to any other user who runs ps. Even on systems without such a version of ps, it is unwise to assume that there are no other methods by which users can examine process environments.