It may indeed be an accent thing--I often end up turning the p in "yep" and "nope" into a glottal stop (so it's more like "ye'," as opposed to "yeah"). And it is obnoxious, usually intentionally so, which is why it's usually Gabriel's schtick in my fics.

ETA: Now that I think about it, the way Jensen says "Nope" in the new "Fist Bump" promo is about the way I normally pronounce it.