IQ does not suffer in the slightest. In fact, I believe that extension tubes
increase your IQ. This is just my own gut feeling, I've never read anything scientific or official saying this, but it stands to reason that a
lens will be better optimised further towards the middle of its focal range, and my results seem to confirm it. (I'm talking here about the situation where, for example, your subject is 3.4 or 3.6 metres away. In
theory, it's within the 3.5m MFD of the 400/5.6, but in reality the
lens is only just barely able to focus on it. With a tube, however, the
lens is well inside its focal distance range. Be all that as it may, tubes certainly don't
reduce IQ.
Other effects? You already know the main one: loss of infinity focus. You lose some
light as well. I've never measured this and can't tell you how much exactly, but you do sacrifice a small amount of
shutter speed for any given
light level and
aperture/
ISO setting. You probably won't notice this in practice. Finally, in theory, you get some vignetting, but that won't apply to your 40D - it doesn't seem to apply on the (larger sensor) ID III either, doubtless it's only if you go full frame that you see it.
Short answer: go for it, they are very, very useful!