Wow, that was a long research trip 
After everything failed (complete uninstall and reinstall of MT, reset of TCC database entries… and more experiments) I came across these sqlite commands and customized them.
Disclaimer: use these commands at your own risk. They directly modify internal MacOS settings.
Before editing the TCC database, it might be a good idea to back it up. Just in case:
cp ~/Library/Application\ Support/com.apple.TCC/TCC.db ~/TCC-Backup.db
Then, add System Events Automation permissions for MIDI Translator Pro:
sudo sqlite3 ~/Library/Application\ Support/com.apple.TCC/TCC.db "insert into access values ('kTCCServiceAppleEvents', 'com.bome.miditranslator.pro', 0, 2, 3, 1, '??', NULL, 0, 'com.apple.systemevents', '??', NULL,1571402310);"
You may need to restart MIDI Translator Pro.
And voila, now it works! I now have the necessary entries under ‘Security → Automation’ and Midi Translator executes the scripts perfectly!
Finally a success, I had almost given up.
Here is another command to read the status of the automation permissions:
sudo sqlite3 ~/Library/Application\ Support/com.apple.TCC/TCC.db "select * from access where service='kTCCServiceAppleEvents';"
and to delete the generated entries:
sudo sqlite3 ~/Library/Application\ Support/com.apple.TCC/TCC.db "delete from access where client like 'com.bome.miditranslator.pro';"
Thanks for your help! I am so glad that everything is working now.