As you said, You need to clean out your rockers thoroughly, from the access holes hidden under the carpet. After that, flush them with clean water from a garden hose and make sure they drain well. That is the best thing you can do to prevent more rust from forming inside the rockers.
Make sure to brush away any loose rust and treat the rusted steel with a rust converter or something to dissolve it, like naval jelly. Then paint over the bare metal.
Your idea of drilling new holes would be, at best, of no help, and at worst, a new source of rust. Anytime you remove paint and galvanizing, exposing bare steel, you are inviting rust to begin.
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