But not too deep:
She's cried in File 1 (Case Aftermath), File 9 (Shinichi), File 16 (Case Aftermath), File 48 (Shinichi), File 71 (Shinichi), File 95 (Shinichi), File 143 (Case Aftermath), File 260 (Shinichi), File 334 (Shinichi), File 353/File 354 (Flashback – Case Aftermath), File 379/File 380 (Shinichi), File 428 (Shinichi), File 482 (Shinichi/Case Aftermath), File 650/File 651 (Shinichi), File 727 (Shinichi), File 745/File 752 (Shinichi), File 884 (Flashback – Shinichi) File 921/File 922/File 923/File 924 (Flashback – Frustration/Case Aftermath/Shinichi) and File 931/933 (Zombie Movie and Zombie encounter). Thats a total of 20 times—in a total 27 Files—12 times exclusively due to Shinichi, 4 times exclusively due to the aftermath of a case, 1 time due to Shinichi and the aftermath of a case, and 1 time when the aftermath of a case, Shinichi, and simple frustration all happened across 4 files... and then there were two instances due to zombie movie and a "zombie" encounter. I don't think I missed any, but I could be wrong about that. She cried in 6 of the 130 Files before her second suspicion arc began, cried only once during her second suspicion arc, cried 5 times between her second and third suspicion arcs, cried during her third, just one case-long, suspicion arc, and has cried 7 times since the last suspicion arc. In all, she's cried in 19 of the 273 cases, and 27 of the 945 Files.