Tubes will work just fine with your 400/5.6 Wayne. See
this thread for an example shot using a 400/5.6 and a 25mm tube. There is a heap of other examples over in
this thread, all taken with a 500/4 and either a 25mm tube or stacked 25mm and 12mm tubes for 37mm in total. Many of my other small bird pictures (posted here and/or on my website) use an extension tube, I often can't remember which ones as it doesn't show up in the EXIF.
For small birds, tubes are pretty much an essential unless you are using one of the very few longer
lenses that have a decent minimum focus distance (the
Canon 100-400 is an example). Most (all?) longer primes have crazy long MFDs, presumably in an effort to keep the overall physical length of the product down and thus not offend the primary buyers of these
lenses: sport photographers.
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!