It would be quite valid to add a few extra costs to the design of any aircraft that makes deficits in the original design. Be that a gun pod because the airframe lacks a gun, a jamming pod because someone realises it needs more active EW, exteranl tanks because it lacks the range for the ops we require or targeting pods, wide spectrum EO or whatever.
We've been here with almost every previous platform; bolt-on goodies to do the job. But, of course you can't easily do bolt-on goodies to a stealth platform. If you want an example, look at the EO window under JSF's chin and the radome and then discuss the requirement for their narrow band apatures and what that means in operations terms.