I’ve encountered a few WordPress blogs that had been bombarded with spam comments (some over 200k comments – taking several gigs of db space). Usually these comments accumulated over a few months or years (many using Akismet) – but if you’ve tried to delete thousands of comments through the WordPress admin, you might have noticed it taking very long and timing out.
Having these comments exist in your WordPress site only increases the size of the database, causing backups and migrations / upgrades to take longer. Unless you have plans to review thousands of comments (if so, you probably have too much time on your hands) you should be able to delete these in my opinion. The fastest option to remove the comments that I’ve found is to delete them from the database side (MySql).
Chris Bitting 