The Animation Nodes add-on works on metaballs using the Mesh nodes. So you can do all kinds of things with them. Most of the things the modifiers do, if not all (but much more for sure).
The latest version is here.
There's plenty of resource on Youtube to learn how to use this big and powerful add-on. Even the developer Jacques Lucke has a Youtube channel full of it. The documentation is also very useful.
Actually, even Sverchok works on metaballs, so I guess you're pretty much covered. Sverchok is similar to Animation Nodes but offers other possibilities. And the resources are even more extensive. There's a Documentation too and Jimmy Gunawan made so many videos, any effect you can think of, he's certainly got one for it. Heck, he's got a whole series with Metaballs !
There's a bit of a learning curve for both of these add-ons, but every minute spent on them is worth it. They're arguably among the best free add-ons for Blender and we won't have a built-in "Everything Nodes" anytime soon.
If you're stuck on how to do a specific effect with any of these add-ons you can ask in another question and give a link in a comment below. But first learn the basics.
Good luck !