To think it is rude of shop assistants to say ...

[rosiecam]

... to say "Thank you for waiting" in a loud voice to next customer when previous customer who has been slow for whatever reason is still very obviously within hearing?

To me it means "I'm annoyed with you for holding up the queue, and I want you to know it, but I'm not allowed to say it, so I'll pretend I'm being polite to the next customer"

[MyPeriodFeatures]

I think you are overthinking this!