There is a problem, I think: as the game grows more popular, more people show up for sanctioned events, and tournaments are getting long.
There's a lot that can be done to minimize the problem, though. If rounds are a strictly enforced 75 minutes, and you stick to 10 minutes between rounds, you can run 6 rounds in about 8 hours 30 minutes. (Even if you slip a couple of times, 12 hours for just Swiss rounds is excessive.)
And stores need to be realistic about the size of the event. If the tourney staff is very experienced and can manage more people efficiently, great. But if they're novice or inexperienced about handling large groups, then they need to put a self-imposed cap at a specific number. We ran 4 rounds of swiss, plus a top 4 cut, yesterday and we opened for reg at 10am, started the first matches at 11:15am, and we were out by 8:15pm.