I'd be fascinated to see the kind of SEO that would go on if this took off. "Bad news-- we're a top 100 hit for several of our main keywords. We'll have to change our URL scheme again."
High page rank pages / sites could start holding competitors' pages hostage by linking to them. Maybe we'd see a resurgence in Flash.
search engines can follow links (sometimes) through flash. and search engines know what the most popular sites are even without counting number of links to sites, so hiding links through flash (or js, whatever) wouldn't help