Ferret, you are correct. No issues will be apparent at the altitudes most bikes operate, even up to the 12000ft mark. EFI (depending on its complexity) will compensate somewhat for altitude by leaning the mixture and, perhaps, adjusting timing. This optimises the fuel burn. Normally aspirated carbs, as fitted to, say, an old CB750, will not compensate for altitude. If your bike is fitted with normally aspirated carbs and you spent all your time at altitude (Rocky Mountains or wherever) you could change jet sizes to suit. This would mean a more optimum fuel burn. This is what EFI does for you.
However if you happened to have a dynamometer in your back pocket, and you used it to check HP at intervals during your climb to altitude, it would soon become apparent that as you climbed higher HP decreases. More so on the carburettor bike than the EFI bike. But still both bikes will lose power. However unless you are doing timed runs on a drag track it is unlikely to be noticeable. This HP loss occurs because for every induction stroke the same volume of gas contains less oxygen. Strapping on your portable oxygen mask and continuing the climb on that twisty new road to the peak of Mt Everest would mean that at some stage during the climb you would notice a HP decrease, and perhaps the engine might even give up the ghost completely. I say perhaps 'cause I don't know when this would happen, but it surely would.
Cheers
For my US brethren when I said "gas" above I did not mean petrol (or flatulence) but simply "air".
