But... The .nomedia file convention is for, well, media applications. Image viewers, video or music players, etc. MiXplorer is a file manager, and with root capabilities, so it makes sense it can see everything. Can you explain better what the problem is for you ?
For example, I have .nomedia at the very root of my storage so that Android and any third-party media-capable application stay out of it ( no indexing, no searching, no thumbnails, no nothing, stay away ), but I want obviously my file manager to be able to see any and every file.