How to get rid of "The disk you inserted was not readable" and auto ignore it? (without installing apps)
Due to no answer yet, I did find a workaround and want to share here.

(1) Resize the external drive and create a small 100MB Apple_HFS typed partition on it. (label the partition with the name dummy).

Explanation: Since there is a recognized readable partition in the external drive now, there will be no warning popup at all and will auto mount it as /Volumes/dummy/. 

(2) Create a shell script in the PATH with the name vagrant-up.sh which has the following content:


diskutil umount /Volumes/dummy/ && cd ~/vagrant/myVM/ && vagrant up


So to run my vm, simply execute vagrant-up.sh.

That's all. It works well so far.