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How will this affect the interlinking/PR of my site, if any....
But sub-domains will be easy to promote.
sorry totally wrong, PR is passed by links either internal or outbound, so if there is a link to the sub-domain pr is passed.
personally i'd go just for directories myself, i think loads of subdomains is a bit spammy unless the site is huge, i don't think 5000 pages is huge - although it is large of course
If you get your directory structure right you can boost your rankings, by using your directory structure to create "descriptive" URL's that help the SE's "categorise" your site.
is far more descriptive to a SE than mysite.com/tyres.php