Even though Alphonse can't produce tears, because of the armor, he can certainly go through the motions of crying. At a few points, in their pursuit of getting back to normal, Alphonse would doubt the journey and feel the pursuit would be a lost cause.
While walking beside his older brother, Edward, Alphonse suddenly hits an emotional wall. He stops abruptly and stares at the floor.
"Al, what's wrong?"
"I can't do this, Brother. What if we can't get back to normal. What if what we're doing is wasted effort."
"What are you talking about? Of course we'll be normal. You'll get your body again."
"You don't know that. How can you be so sure? The Philosopher Stone is a dead end, trying to create a body would do more harm than good, my body is at the gate, but how do we even open it without committing the taboo again? There is just no way?"
"Come on, Al. Don't lose hope, not yet." As Ed says this, Al drops to his knees and falls to the floor. Edward sits beside Al and props his upper body on his lap. Immediately, Ed could hear the soul of his brother echo sobbing. Despite not being able to physically produce tears, Al begins crying.
"I'm so tired of being in this armored suit. I want to feel your warmth again. I miss everything about having a human body. I'm so sorry you had to sacrifice your arm for me. Wish we had never committed the taboo in the first place. Why is it things have to turn out so wrong?"
"Al, just have faith. I believe we'll go back soon." After Edward says this, he simply sits in silence, letting Alphonse cry as much as he wants to.