Is this going to murder those fancy shell scripts that self-extract a program appended to the tail, which is really just an encoded blob of some kind, presumably compressed, etc.. ???
Not if it was done competently. Shar files and the likes shouldn't contain NULs, even if they contain compressed data. The appended data should be binary safe.
And in case your data does contain NULs, presumably one could add a layer of base64 encoding. Not nice for the filesize, but also much less likely to upset a text editor when the script is opened (even in the absence of NUL bytes).