I was wondering if links pointing to a hub from another Hubpages sub domain will count or improve your search engine rankings? i mean are they recognised as backlinks?
Most backlink checkers are fairly unreliable, and even if they did find most backlinks (they don't), they don't know which backlinks Google indexes (step one) or considers relevant for any particular search query (step two). So I wouldn't put too much stock in whether any one backlink tool has found certain links.
We do know that Google indexes cross-links within websites*, so there's no reason why it wouldn't consider links between subdomains. How much they count? Ah, would Google deign to tell us that? Of course not.
*By the way, just as an experiment, I tried searching Google for:
link:[url of one of my hubs]
without the brackets. I noticed that Google included as backlinks the links that are shown in someone's activity stream listing hubs they've recently commented on. So there's a way to get Google to index a new hub: use social media to promote the hub, have good enough content to earn some comments, and hopefully, Googlebot will spot the link to your hub in someone else's activity stream. I doubt that backlink counts for much, but it should at least get your hub indexed initially.
Note that Google's link: selector only shows a tiny fraction of the links it actually knows about. Google is sssneaky.
WMT shows thousands and thousands of links coming to my subdomain, but only a relative few from within the subdomain. Of those external links being shown the vast majority are from other subdomains and a bunch from HP itself.
WMT is counting those links from other subdomains as external links, not internal ones, and it could be that the SE algorithm is doing the same. Or it might not.
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