Like peter says most brands need their permission to be used for anything, Coca Cola is one that defends it vigorously, I believe they even have there own colour Red Vinyl.
Difficult to say really, it is the responsibility of the shop owner as Peter says and if they understand that they may be told to remove it and are happy with that then I suppose you have done all you can. I normally find once I have explained the copyright issue the customers change their mind anyway.
I’m not 100% sure I would do it if still asked, problem I see is that if it had to be removed would the customer then start to bad mouth you ?? Yes you explained everything to the customer before the work was done but they are hardly going to go round telling people that are they.