It doesn't make them stronger or weaker. They have spent a significant part of their lives not fitting in. They have been attacked and forced to kill. They have been forced to leave their only support system behind. The crying makes them seem more believable because after all they are still just young teenagers.
I don't think it is necessarily a step to becoming stronger or weaker mainly because it depends on the views of strength that the reader has. If someone who views showing emotion as a growth and strength, then yes. The fact they were able to cry in front of each other could be construed as them growing together and gaining strength as they certainly grew closer showing that much emotion. If someone views the showing of emotion as a weakness, then they would think they were weaker for having shown that deep of emotion, especially in front of another male. It all depends on ones viewpoints.
Johnny and Ponyboy have run away after the killing and left behind everything they've known. Crying shows that they're upset and sad after these developments; it's not a process whereby someone becomes strong or weak.