I see lots of people riding those tiny wheeled BMX bikes essentially stand to pedal nearly all day when sessioning for long periods. Though, it's hard to speak to the long term effects of their behavior considering how high impact the sport they've chosen is.

However, I tend to agree with the other respondents in saying that for your longer distance riding you'll be doing you should spend a little time figuring out how to ride in the saddle. I think you'll find it easier on you physically and, provided your fit is right, more enjoyable.

While standing, do you typically find yourself spinning smoothly or do you feel as though you're constantly accelerating? If you're not pedaling much and riding while standing, seems similar to the stance I've seen some take on a bike of that type anyway.