If Fetch like Google is also giving a 301 - I would mark them as solved in WMT & check if they re-appear.
If you click on the i next to the redirect message in Fetch like Google - it shows the type of redirect & the page it's redirecting to. I assume you checked that this is also a 301.
I have a similar issue on one of my sites - if a user gets to a non-existing url - the server first tries to find out if the page exists - if it doesn't it's redirected to a 404 page. Although technically it is a 301 - WMT sees them as a soft 404 as the destination page is a "Page not found" type of page (called 404.php) - which (quite ironically) renders a 200 status.
On the destination page - do you mention somewhere a message like "page not found" or is it just a plain category page?
The SEO impact is difficult to assess - Google says these pages are mainly wasting the bot's time as it's indexing pages that do no longer exist, not sure if it is also affecting rankings. As you did the crawl with Screaming Frog, I guess you are also removing all internal links to these redirected pages? If these links disappear, and as the content was thin, I suspect you don't have many external links pointing to them, so the problem should disappear after a while.
rgds,
Dirk