How will Apple's switch to ARM (Apple Silicon) affect compatibility with Linux / Unix tools and APIs?
The betas of Big Sur (on Intel, at least) have the all the same Unix underpinnings and other components as before. (Even python 2.7, which was widely expected to be removed!)
You would hear a lot of noise it if Apple ditched its 'certified Unix™' status.
Xcode isn't going anywhere either, so you can compile any Unix code you've got source for.
As for X11, that hasn't been updated for years, so will have to run in emulation until someone recompiles it (hopefully fixing the Retina display issues while they're at it).
There may be teething problems, particularly in the early days. But I'd say that recompiled code is likely to have fewer problems than Rosetta emulated stuff.