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Yes, otherwise you'll be running extremely lean, and they come lean from the factory to begin with. I wouldn't go with a dealer "re-flash" though, as far as I'm concerned they're a waste of money if you do future mods. I'd go with a fuel management system. I personally like the Power Commander, but there are other good ones out there as well.
Will I need to do a remap, if I only do a stage 1 air cleaner and slip on exhaust?
In a word, yes. A power commander or sert or some other type of fuel management will be better. As long as you only change the intake and exhaust, a canned map will most likely give satisfactory results.
If you're not going to do motor mods you could get away with an XiED for about a hundred dollars or less if someones selling one in the classifieds here. Nightrider.com