> what's stopping some employee from something like Mathematica from taking the source code and having an agent port it to open source

Laws against theft. Also the same reason employees don't release the code on pastebin or something.

> Who owns an algorithm?

The org or person who was granted the software patent. https://en.wikipedia.org/wiki/Software_patent

> Will everything get copied eventually?

If we're lucky. More likely everything bitrots as technical capabilities are lost. Slowly at first, then quickly.