to masturbate.
"Have a good one" being an alias for "Have a good wank", or more precisely "Go f*** yourself".
It seems that some people who are store clerks are embittered by the fact that they are store clerks and seek solace in this ambiguous flippancy.
VIP: Nice suit you are wearing eh?
Clerk: Thank you sir
VIP: Could you call me a cab?
Clerk: yes sir
VIP: good bye and have a nice day
Clerk: have a good one sir
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