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I don't think there is a penalty but there is no benefit and it may cause problems. Why do something unecessary if you don't have to?

Once a page is indexed it will be displayed no more than once for any given search term but can rank for an unlimited number of search terms.

Yes. Every page, even those on subdomains, must do a 301 redirect to their new URL or else they will be considered new pages and all SEO value they have (i.e. incoming links) will be lost.