How can I prevent line numbers from appearing in .bash_history?
Update: The recent edit you've made to you question shows the following line being in your .bash_profile file:

export HISTTIMEFORMAT='%y-%m-%d-%T   '


Remove this line to stop the timestamp from being added to the ~/.bash_history file.



Original Answer:

As HISTTIMEFORMAT is not set by default, up to an including macOS Mojave, you'll need to check one of the following files to see where it was added:


/etc/bashrc
/etc/profile
~/.bash_profile
~/.bash_login
~/.profile
~/.bashrc


Removing the line that has HISTTIMEFORMAT from the file that has it will stop the timestamp from being added to the ~/.bash_history file.

Note: The dot files mentioned in the $HOME directory are hidden and some may not exist.