I can only guess, what with fragmentions being a new-ish and experimental idea, and the minutiae of search engine algorithms being hard to pick apart.
Google and Bing tend to ignore fragments, with the exception of hash-bang URLs used to crawl AJAX content, so from that perspective it should be no problem. On the other hand, the ## construct is not valid for URLs, and that may or may not affect your SEO score.
Wish I could be of more help, but if SEO is critical to your sites, I would advise caution.
Is there no way for the plugin to be coded to hide fragments to bots?
Just leaving the plugin on should not hurt your SEO.
What the bots do see is the *links* to fragmentions. If these links are on some other site, it’s not your problem to worry about, but if you’re hosting them yourself, then they may be parsed by search engines.
While browsers take markup like <a href="http://link.to/path/##hello+world"> just fine, that link is invalid according to the URL specification, and I have no idea if bots will be permissive about this kind of stuff.
I guess time will tell or we should ask Matt Curtis. XD
