I'm sure that somewhere along the line, a highlander or two probably took to piracy. Whether or not they wore a kilt is anyone's guess. Based on the time frame of the classical pirate age (late 16th to early 18th century), it would have been the time of the great kilt in Scotland. I can almost guarantee they would not have worn that garment though, at least not often. The areas of the greatest piracy tended to be pretty warm (for example, the Caribbean). Not to mention all the cloth that could get caught in rigging, etc.

My guess is IF they wore a kilt at all, it was the phillabeg, or in other words, the bottom half of the great kilt.