Hi Richard
If the content about various subjects is distinctly different then even tho' the site structure is kept similar you should be able avoid duplicate content by creating quality content for each page of each site and following best practice basic SEO.
Even tho' the hierarchy is the same you'll probably want to include keyphrases in your navigation where appropriate and in url structure, headings, meta tags, images, file names etc as well as page content. But too rigid a structure, even tho' it's easier to manage, could effectively stultify any natural growth of these sites and affect their value and of course the chance for back links.
AND If there is a move to employ cookie cutter content, either manually or though consuming feeds etc you might struggle with not only the duplicate content issue but for a range of other best practice areas.
Additionally you'll want to be careful with linking and hosting between the sites so as not to be perceived as linkwheeling etc.
Best
Shiv