My youngest has had dozens of procedures and uncountable sticks with various needles. We weighed decisions re: her care in part based on which could end up leaving her worse off, doing or not doing.
Re: the H1N1, given the serious complications that some are experiencing, I'd consider that what's involved in sustaining life in a critical care unit by far surpasses a minor, quick shot. So if it were me, I'd take them for the shot.
Re: seasonal flu, not getting the forms of flu going around last year is no guarantee of not getting what's expected this year. While the chances of complications are less than with H1N1, there is still a lot of discomfort involved.
Maybe, if you do take them for the shots, explain to them that the quick poke can save them a lot of misery. They are old enough to understand this, and during the course of their lives will encounter other situations where taking a moment to do something unpleasant can be a huge help to them in the end :)