We don't use balloons for doing the kinds of observations that wallace and turbo discussed because balloons are not sufficient for those tasks. A very stable platform with a very well-known and attitude is absolutely essential when looking at the stars. Balloons are not stable. Since those UV and gamma ray instruments are quite expensive, we also need to platform to stay up for a long time. Balloons come down, sooner rather than later.
We do use balloons for a lot of measurements of the atmosphere. Weather balloons and Earth-sensing satellites perform complementary roles. Satellites that look at the Earth have a broad view of the Earth, while balloons only sense conditions in their immediate surroundings. However, balloons measure things like ozone concentration directly. The observation is much less direct with satellites. In fact, there is another name for data collected by satellites: "remote sensing". The science behind remote sensing is always viewed as suspect initially. Remote measurements need to be verified against some trusted measurement. Direct measurements such as those made by radiosondes, dropsondes, and rocketsondes provide the sanity check needed by remote sensors on satellites.