So 1000x1000x9x48000 multiplies and adds per second, that's 432 Giga-Multiply-Accumulates per second??? That is high-end FPGA or GPU territory. Axoloti Core is far from that.
I do have dreams about Axoloti targeting FPGA, or GPU, but really, don't hold your breath...
The art of audio dsp programming is finding a good balance between accuracy and computational load. I suggest doing non-realtime simulations first, and then try to reduce it drastically with a minimum impact on the result.
I believe Axoloti is capable of one dimensional digital waveguides, but in 2D it would get extremely limited.