From http://www.1stbrigadeband.org/Instrument_11H.html
Allen valves exchange rotor height for volume to take advantage of the fact that volume (and hence, weight) increases as the cube of the radius in the case of a round-port valve while it increases only as the square of the height in the case of an oval valve.
However, the ovalization in a typical Allen valve is much more severe than the ovalization in a Conn short-stroke piston valve. I suspect that cornetists grew to despise the negative acoustic effects of it. I've never read anything that that states that Allen valves presented a negligible effect on acoustics.