I'd have to say I'm guilty of working in files where everything is layer1 layer2 etc, but if I'm doing client work, everything is always named and put in folders according to section. This slowly happens in the design process, but it usually cleaned up and perfected before the design is sent off to the client or a developer. Some of the coders I work for don't need much direction so I admit I've slacked off a few times, but it is much easier to work with a document later when everything is named and in its place, thats for sure.

I don't think it really takes much time out of the project to name layers etc, if anything it saves you in the long run.