If you have 1000 domains hosted on the same IP, some belonging to the same webmaster, the only useful info Google has to work with to run a full link analysis is the link graph (Google has its own copy of the web) and whois info.
There's no proof Google checks whois, but after all Google is a registrar and has access to that data.
Even if you have 10 sites about 10 different topics that don't crosslink or link trade with the same set of websites, a Googler may look at your entire domain collection to pass judgement on your character as a webmaster.
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