Breaking this down a bit: I don't know the exact spread, but a lot of federal district judges handle the criminal side of the docket themselves. In my district, this was the default assumption, but judges were obviously happy to loop in clerks who wanted some criminal experience, and/or would seek clerk input on non-rote disputes. So at least on the federal district court side, what you care about isn't whether a judge "does" criminal cases, but how a judge handles her criminal docket.
Outside of the "standard" federal district judges, there are plenty of specialty federal courts and/or state courts that hear civil matters exclusively. The question of whether clerking for these courts would "hurt" you has no simple answer; it depends on the kind of prosecutors' office, how competitive things are, how weird the hiring cycle is, etc.
I suppose that some prosecutors' offices might wonder why you spun your wheels outside of your preferred subject area, but plenty of people do other things before becoming prosecutors.
Tl;dr: if you're interested in becoming a state prosecutor, and your question is "would a federal clerkship with a district judge who uses his clerks mostly as civil motions clerks actively hurt me?" my answer is "probably not."