The SP Page Builder forums suggest that sh404SEF indexes all website links including the SP Page Builder front-end editor pages. If this is true, then Google probably also indexes them to the detriment to SEO, no?
sh404SEF does not index anything. At all. That sounds like a lot of confusion happening on that forum :)
sh404SEF simply converts non-SEF URLs as created by Joomla and extensions into SEF ones. If you do not have sh404SEF, that job is done by Joomla itself (sh404SEF just does it better ;) )
So whether you have sh404SEF running or not does not change what Google indexes from your site (unless of course you use sh404SEF to hide pages from Google which is one of its features).
But out of the box, search engines indexing is about the same with Joomla and sh404SEF. The only real, practical SEO difference is that with sh404SEF you know you won't have duplicate content.