If I do the query
http://search.twitter.com/search.json?q=from:TopTweets%20-filter:links
as of early February, I'd get back tweets from TopTweets with any tweets containing URL links filtered out. Something changed, and now using -filter:links will return some results that have t.co links in them.
The non-inverted form seems to work correctly, returning only results that have links, but no linkless entries. The docs at https://dev.twitter.com/docs/using-search don't specifically address a negated "filter:links", but they do list some operators that can't be negated and filter isn't one of them.
Updates
- Acknowledging that it seems to miss a link here and there and reporting to team. In the meantime, you'll just need to discard those results.