First of all, beautiful map. I really like the style.
Second, I like your labels find and, stand-alone, the descriptive labels are better than numbers - but that might not be the case when it's presented in an adventure format. The font looks like papyrus, which is the butt of some jokes I think I kind of like the font...
I have no experience with this but I was under the impression that some publishers (Paizo comes to mind...I sat in on a Sean Reynolds mapmaking session at Paizocon) did the labeling in Illustrator after map completion (I don't doubt this is the source of much of the mis-labeling that goes on in their maps, which are flawless otherwise).
In general, though, I'd do whatever the heck the publisher wants you to do. They're typically pretty picky about whatever process they've chosen to work with and want it done their way - for good reason, I guess. If they've expressed a preference then I'd stick with it. Having your descriptive labels in a separate layer probably isn't a cardinal sin, though, and it might help the poor guy trying to label it in Illustrator if that's what they do with it.