As far as I know, Tunnelblick cannot affect macOS prompts such as those asking permission for Java or Terminal to access Tunnelblick. That's a security feature of macOS.
But skipping Tunnelblick prompts so the prompt is never shown even one time can be done for any prompt that has a "Do not warn about this again" checkbox.
You'll have to dig into the Tunnelblick preferences to do that. Showing a prompt is skipped if a preference corresponding to the prompt is set to "true". (Note that some of the preferences are per-configuration preferences -- that is, there is a separate preference for each configuration.)
For a list of all such preferences, you can look in the Tunnelblick source code. The
defines.h file contains two lists; one for non-configuration-dependent preferences, one for per-configuration preferences. That file changes, of course, as new preferences are added or made obsolete and other changes are made.
To set a preference "true" you can use this command:
defaults write net.tunnelblick.tunnelblick NAME -bool yes
to un-do that, you can use this command:
defaults delete net.tunnelblick.tunnelblick NAME
For per-configuration preferences, NAME is the name of the configuration followed by a hyphen followed by the name of the preference, e.g. VPN_NAME-PREFERENCE_NAME.