Any negative meaning of the words "What is the damage"?

If used when buying something, "What is the damage?" simply means "What is the cost?" In this case, 'damage' implies that the cost is 'damaging' the speaker's finances.

This is usually used in a casual, friendly way.

As with anything, the speaker's tone or the context of the situation may show that the speaker is upset, but the words themselves don't imply that.

One who speaks of "What is the damage?" is not necessarily unhappy.

The speaker simply means to ask how much something that has been ordered or purchased cost.

We would say it in a touch of a tease, more to liven up the atmosphere instead of a complain.

You would use that only after something has been ordered or delivered (after eating at a restaurant for instance).