Pypy gives you at best a single-digit speedup, and requires carefully going through your dependencies and checking all your codepaths. That's rarely a good value proposition for a business - if you're growing fast enough that performance is an issue, you're going to need a bigger speedup than that pretty soon, and if you're taking the time to go through all your codepaths, it doesn't cost a lot more to make a bigger change like switching languages entirely.
I worked on a project (15+ years ago) that used Jython to put a web front end on GDS systems (airline reservation mainframes). It was in production and being used in some of the largest travel call centers at the time. The whole thing was built in Jython.
I'm guessing almost nobody uses it for their SaaS, but outside of that, these runtimes do see some use.
[0] https://www.spotfire.com/