Does the unused postmeta affect the speed of my database?
Anything in your database affects the speed of your database. The question is how much of a slowdown, and if the amount of data is significant enough. Unless your having a huge amount of metadata it will not affect the speed of your database very much.
Does removing the postmeta in this way affect anything else I would later regret?
Anything that uses your postmeta data will be screaming for help. Assuming your only using your postmeta to display extra information, it shouldn't be a problem. I haven't tried the code which is mentioned in your link, but the author him/her self doesn't guarantee if it works.
Is there any practical way to test this on a database with 1000's of posts and multiples of this in postmeta rows?
Like the orginal poster mentioned "Test it on a development server with dummy data." If it works on a small set of data it will also work on a bigger set of data (but it will take longer).
If your looking for a way to delete postmeta for only certain post you can take a look at delete_post_meta. You can also try plugins like WP-CleanFix, WP-Optimize, and WP-CleanUp.. to optimize and clean up your database.