Will papers published in other sub-disciplines matter for graduate admission?
Undergraduates are not generally expected to have already figured out exactly what they want to do in research, so it's unlikely that there will be any concern about the fact that you've worked in multiple areas.  The fact that you've been involved in research and published papers at all is a very good sign, even if it's not in exactly the field you are applying to be in: it means you're motivated and inclined toward research and have been able to accomplish significant things already.  In short: don't worry about it, but celebrate that you've got such a strong background!