If its got bubbles, it probably already has holes. Problem is when vinyl tops age or have been scrubbed too much in cleaning attempts the waterproofing wears off and they become porous. Also they tend to lift under any moldings as they shrink and the adhesive gives out. From there water works its way under and gets trapped.
Even just the daytime to nightime change in temperature can be enough to cause condensation and contribute to the rust problem. Waterproof car covers will do the same. They trap condensation under the cover and the car stays wet until the cover is removed.
So what's the answer? Repair it. The sooner the better. Even if you can't do it right. Do something to stop the rust for now. Take off the top and moldings. Clean up the metal and brush some POR15 over the spots. That will stop the rust for now. Otherwise clean it up, sandblast the rust, weld in patches if necessary and use epoxy primer. Then continue with any body work, high build 2K primer, sealer, base coat and clear.