Yes. I've also used this when leaving a job, albeit with a slight modification since the job did not provide fish. I suppose you could read it with the subtext that the dolphins are saying "see ya suckers" but I think it's more appropriate to read it as the dolphins actually saying "thank you" even though things didn't entirely work out.
One of my reports was a hardcore HHGG fan, including carrying a towel on towel day. He signed off with the "so long and thanks for all the fish", and I don't think anyone read anything negative into this.
In fact, while that was some years ago, it was a tight-knit team and we still meet up for dinner with the original team members about 2-3x a year :)
I had a coworker say this when quitting. Most people that knew the reference interpreted it in a negative way. I would not recommend using it because of how ambiguous it is
tbh I had never thought carefully about it until now. I always got excited hearing it from other people thinking "Oh another person who likes Douglas Adam's book!"
I'm kind of glad I read this thread though, I can see why it could stress people out.
If I remember correctly, the dolphins had tried to warn humanity without success and eventually gave up and left, so the “see ya suckers” reading doesn’t quite track.