I've done this before, but i'm afraid I don't quite understand your point.
When you use the Joint Stereo Mode in LAME at bitrates 96 and above, it converts from stereo to joint stereo losslessly, before applying any lossy compression. LAME encodes each channel independently.regardless of whether you use L/R or M/S mode.
The encoder will take the lossless stereo file, then encode it to a lossless joint stereo file, then it will encode it to MP3. (Encoding the mid channel and the side channel independently).
The number of M/S frames in an mp3 file is meaningless. You could have a track thats 95% Stereo and only 5% Mono, but using Joint Stereo over Full Stereo would still make perfect sense. It just means that 95% of the frames will be in the side channel and 5% of the frames will be in the mid channel. This will either save you a small amount of space (if VBR is used), or will give the encoder extra bits to improve the quality (if CBR is used).
Let me ask you, if you think Joint Stereo is lossy, then what makes it different than Intensity Stereo? Why would there be 2 types of Joint Stereo, if they are both lossy?