In general, I think poker etiquette should be respected in live and online play though it's not easy to draw any line when playing on the internet, hence the word "Unspoken"!
I also think that the question in hand has more to do with the game play than with the etiquette. I would say that 99.99% of players would never wait for a sitting out player to come back after having played for so long to get to a HU situation where they could finally win an MTT, a win that does not come along that often.
In certain situations (CC events for example), I might wait for my opponent, otherwise, I don't see why, especially that we're both taking home a nice prize.