The idea is to reduce footprints, and hiding of whois information saves you not only from Google directly, but from your competitors too who may want to identify all of your domains and report you accordingly.
You can split your content on the same domain using folders or subdomains if you want to make them niche specific. However, I think you can still rank general topics, as its pages that would count here, the more relevant to searched keywords they are, the better they would rank.
Online tool would be moz, you can get a free trial account. However, if you want software programs, then longtail pro and traffic travis would also offer what market samurai does, though for backlinks, they would be using seomoz data whereas market samurai uses majestics.
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