Is he still considered Junior if...?

…he has one more mn than his daddy? We have decided that if we have a boy, his name will be [name]John[/name] [name]Paul[/name] like my husband. However, we are contemplating the idea of giving our children two middle names, but if we did that, would our son still be a [name]Junior[/name]? Any thoughts?

No. A junior has the exact name as his father, which is why the Sr/[name]Jr[/name] designations are used to differentiate. If you add another middle name, that differentiates the two.