The very long URLs created by Urchin and other web analytics was one of the problems that URL shorteners were created to solve.
Whether short URLs have a "malicious" effect is a topic for a different discussion, but whatever the effects of URL shortening, Urchin parameters are not among them.
Urchin parameters certainly do make it harder to detect duplicate URLs, which would be pinboard's primary problem with them. However, so lots of other URL parameters like sessions, landing page refs, etc.. Urchin's are just the most common ones.
[Disclosure: I work for awe.sm, which provides social media analytics using, amongst other methods, short URLs]