No, SMS-Utilities don't run any user scripts for security purpose.
Yes You could periodically list all SMS via 'gsmctl -S -l all' command and start any user script. Make sure that SMS-Utilities don't delete all incoming SMS. Also I recommend to leave at least 5 free SMS slots in SIM that new SMS could come to SIM.
May I ask what functionality you want to achieve?
Maybe SMS-Utilities or another service could handle it for you.