I feel like the game assumes that most player's only motivation for helping Judy out is... to get in her pants, really. Almost like it doesn't actually expect anyone to be invested in the fate of Clouds itself. It just makes the entire quest feel somewhat superficial.
And yes, it hadn't really dawned on me until you pointed it out, but Judy's response to it all is really unhealthy. She just decides to give up and ditch NC after the first setback. In the end, neither she or V actually care all that much about Clouds, they just care about each other. I guess that's sweet, if only Tom didn't have to get killed to make them realize it.
If I remember correctly Judy had more setbacks than just the one with the Cloud coup. Her failed relationship with Maiko, her issues with Evelyn and Evelyns death on top, problems with her boss at Lizzy's, her job in general, feeling lonely in NC, ...