Would the attack even succeed? Part of the reason the hijackers chose the flights they did was to minimize the passengers (not out of concern for them but for their ability to commandeer the planes) and maximize the possible audience for the attack. Both variables would be different with a later attempt.
Actually, there's a practical issue in pulling this off at the correct time because it is not a time when there are a lot of large long-haul aircraft scheduled to depart East Coast airports. The SOTU typically starts at 9PM Eastern Time, which would make your target impact time around 930. This is too late for the vast majority of US-Europe departures and past the peak time for transcontinental departures heading west from the east coast.
I'm not saying that pulling this off is impossible, but planners would have a lot fewer possible flights with which to work, which raises the odds of random factors affecting the outcome. And, you should add to this the possibility of flight delays, which typically accrue through the day. A flight departing Newark, Boston or JFK is FAR more likely to be on-time early in the morning than it is in the evening.
The SOTU is an annual one-off event. Had something gone awry on 9/11, it would have been nothing to call off the plot and try again a week or two later. This is not possible when you are attempting to pull something off at a fixed date and time.