(Unfortunately it looks like VBulletin has stuffed up the example link you gave in that "trying to be helpful but failing" technique it uses so often. But I think we've got the picture of what you meant from the rest of the text)
I don't see why it leads to bad coding practices. Sometimes you will have a folder structure that is several layers deep. Depending on the nature of your site, it may be much easier to manage it if you store things in that way than having fewer folders but each having many more pages in. So sometimes a link to ../ may not be a link to the root, it may be a link to the parent folder - in which case, I'd say it is better to retain it as ../ rather than give a root reference that then has to include the folder name. If you do it that way, your code is less flexible and less reusable, you're more likely to end up with a link to the wrong folder at the next level up.
As for search engines - nope. Search engines, like any other browser with a person using it, can and will correctly and unambiguously parse any correctly formed hyperlink, whether it's a relative reference, a root reference or an absolute reference. Search engines don't have any problems coping with relative links incorporating ../