I actually read something where Lee Bermejo said the crying scene was about showing all the sides of the Joker's manic depressiveness.
Or just "Batsy, can't we all just get along? Let's be FRIENDZ! SRS! FOR REALZ!
But I do wonder if this was another one of Azzarello's Pulp Fiction-esque scenes (a la the elusive suitcase Eddie stole that we have no idea what it contains) where we're just not supposed to KNOW what's going on, like you said, b/c of the unpredictability of the character.
(Oh Gawd, someone brought up Hush Returns and there was some keyboard smashing. ASASDAsffAGf. OK. Breathing now.)