Quoting from http://www.sheldonbrown.com/standing.html:

"Standing pedaling allows you to apply more force to the pedals than is possible seated, because you can rest your entire weight on the driven pedal, and, even more, by pulling up on the handlebar, you can push the pedal with more than your actual weight...but is this a good thing?

Pedaling that hard is very stressful to the joints, and to the bicycle, and usually involves a level of effort that cannot be sustained aerobically. Unless you have unusually good form, it also tends to involve a fair amount of thrashing from side to side, which is a waste of energy. The added stress flexes many parts of the bicycle, and the energy required to do this flexing is not usually recovered when the parts straighten back out."

Additionally, you are quite right that more muscles are used because you are now supporting your body weight instead of the saddle doing this, so the heart rate for the same speed will tend to be a bit higher.