Just to provide the other perspective: One could argue that fewer males applying could be a problem. It's easier to make the argument with a minority group that has been discriminated against so I'm going to go the easier route. If fewer African Americans apply to college, it could be because they have less money and assume they can't afford it, or feel that large institutions (no matter how liberal) are stacked against them, or that they weren't given the tools to get in as easily and so don't even bother applying.
Those are all troubling reasons for someone not doing something. Now, people can and do prefer different things, but sometimes we shape our preferences to what we see as attainable or what we're encouraged toward. So, if only 40% of applicants are male, the question is "why". If it's because they just genuinely aren't interested, that's fine. But society is very complex. Sometimes someone wants something and just gives up on it because it seems like it wasn't meant for them. It definitely happened to me and golf - when it seems like an institution (or parts) aren't so enthusiastic about you, you can start avoiding it.
You're totally right that the world won't end. If there's no underlying cause, it doesn't matter. However, it might be symptomatic of something. It's worth figuring out what's going on since it does stick out. And I haven't heard really any arguments about why it's happening.
Part of this gets down to the question of free will. Let's say that more males prefer to go into trade craft (plumbers, carpenters, etc.) and that's an area you can make a lot of money in and college isn't needed. OK, that explains the discrepancy, but go down another level and is our culture pushing men to trades and women to college - even in slight ways that would cause that effect on the numbers? If it is, is it a problem? The world needs trades people. The world needs college educated people.
I guess on the last part, I do see it as a problem because let's say that males and females have the same average aptitude for things - an IQ of 100 for academia and an IQ of 100 for trades so to speak. If culture is pushing females to college and males to trades, we aren't getting an efficient system - it means that there are some females that have an inherent talent for trades that have been pushed into academia. Here's an example:
Matt - 110 academic; 90 trade.
Bill - 100 trade; 100 academic.
Robin - 90 academic; 110 trade.
Julia - 100 trade; 100 academic.
Now, from those hypothetical inherent talents, Matt should go to college, Robin should go to trade school, and the other two are a coin flip. But, if Robin is pushed towards academia and Matt towards trade, they might end up with scores that are the reverse of what their inherent talent is (let's say admissions scores of 200 for Robin and 180 for Matt). Robin was encouraged to apply herself in the things that show up on an academic score, but really Matt is the one in that example that has better talent. At that point, Robin should be the one admitted - she's become smarter and is better prepared. However, Matt's lacking might have simply been his upbringing.
It really gets into the nitty-gritty of free will and will drive you nuts if you think about it too much. Your attitude might be the right one to take since my head is hurting just thinking about this.