The thread is buried deep in Atari Forums, but from memory the "Mi" stood for Amiga, so it's a shorthand version of "Amiga ST". The logo showed this by using the font of the Amiga logo for "mi" and the Atari font for the rest.
There is also a little language joke. The PCB and original ST core developer (TIll Harbaum) is German, and "mist" means something like "crap" in that language. So basically, the MiST name is intended to have a self-deprecating connotation of "crappy little FPGA board for ST and Amiga"
Edit: the board was developed at first to house an ST core, at the time Till had approached MikeJ for a Replay FPGA board but he did not have any available to give him, so he ended up developing much cheap board for his own use. That little board ended up being very popular. See this thread:
https://www.fpgaarcade.com/punbb/viewtopic.php?id=107