The name Ryujinx is even a C# in-joke of sorts, early iterations of the emulator translated the Switches ARM code into .NET CIL bytecode and then used the standard .NET JIT, which is called RyuJIT, to translate that to native code. NX was the Switches codename, so RyuJIT + NX, minus the T, makes Ryujinx.

They eventually outgrew that approach and rolled their own JIT, but the name had stuck at that point.