PC-98 owner here. I don't know where you are finding the .M files within PoDD and SoeW, but erasing them probably isn't the best idea.
I haven't found a specific program for shutting off OPNA sound channels (yet), but there may be one on Vector (
http://www.vector.co.jp/). You will have to use Google Translate's website translation tool, however, because very little translated/English PC-98 software exists (PC-9800 series computers never appeared outside of Japan). Vector is an excellent site to find PC-98 software on; I've found everything from PMD .m players to i486-specific memory managers. Just make sure your computer is in the Japanese locale while you work with PC-98 DOS files.
If you can't find anything on Vector, then "Hertzdevil", a PC-98 composer, might be able to make you a "silent" .m file. He also knows how to swap .m files around within the code of the PC-98 Touhou games, so I'd try and contact him about making you "sound-only versions" of SoEW and PoDD.
https://www.youtube.com/user/HertzDevil