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I'm no expert on this issue, so don't take what I say as gospel.
Personally, I feel that the contribution XOOPS makes to content management far outweighs that of the search engine optimisations that you achieve by having 'traditional' html pages. The time you save by using XOOPS you can use to optimise your rankings in oter way, for example, by adding yet more content that the engines like!!
I do agree however that, for example, if you were making a site about chocolate bars, you do better on the engines by having the content in a folder called \chocolate\ and an html page called 'chocloate.html' and then by having that full of text relating to..mmm....chocloate, you're gonna do well on Google. Especially if the site is called 'cholcoate.com!' I agree that XOOPS does not allow such naming (that I am aware of) and therefore some XOOPS sites may suffer a little compared to their pure html equivalents.
But, like I said earlier, the CM advantages far outweigh this, in my view, and you'll have so much extra time to find the info you want in your site and the engines will lap it up.