As far as I can tell it should be okay. The forum software I’m migrating from basically allowed users to put whatever HTML tags they wanted in their posts, so my method was to strip out all tags, with a handful of exceptions like <b> (and </b>), <a>, <blockquote> and so on. Currently the only difference between cooked and raw posts in my database is that there are newlines instead of p and br tags in the raw version.
I’ve set a couple of hundred posts as uncooked and started a rebake uncooked posts task on my dev server just now and it does seem to be populating the topic_links table, so thanks! Problem solved.
No, I rolled my own, following the steps of one of the bulk importers.