I have a client that wants to have a cupcake booth (similar to a crepe station) but wants to have their logo appear somewhere on the minis. I've done edible images on gumpaste disks on regular cupcakes before, but don't think that would be very practical.

Is there a way to print something on the cupcake liners? Maybe chocolate disks? Does anyone have experience with this kind of thing? Where could I get printed liners or some other way to get logos on the minis. Any ideas would be appreciated.

why not just pipe their logo onto a bunch of candy melts?

What is their logo? Or do you mean their monogram?

There are companies who make printed liners, google it.