Asterisk queues received DTMFs. However, you are supposed to call autoservice_start on a channel before you doing anything time consuming to make sure your DTMFs won't be lost. (This is what you supposed to do inside Asterisk application. I'm not sure about AGI).

Autoservice (main/autoservice.c) is the thing which reads and queues DTMFs and later when you are done and calling autoservice_stop - it injects these frames back into channel queue so you will be reading them with ast_read.