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I tried typing this URL into Google, and it took me directly to the listed website - not a google listing, but directly to the website. The directory page where this link is found is indexed by google. So, will this link count for PR?
> ... it took me directly to the listed website.
It may look so to you, but you don't go directly to the listed website but indirectly. If it is handled very quickly, you won't notice it is not directly. But, if the site of the nichedirectory is down, and you enter the URL in your browser, you will not see the listed website.
If they are avoiding diffusing PR (hopefully this isn't a violation of starting a new topic within a thread), does that mean they are trying to preserve PR for their own internal links?
The most likely reason is the first one (although a combination of 1 and 2 is also possible). Since they link indirectly, some other sites on the topic will not exchange links with them. So this policy is in some way also counterproductive. A nichedirectory can also get a high PR if they link directly by getting a good hub-like score [webmasterworld.com]. But of course it is up to them, how they want to link.