Using the Dragon Balls to defeat an enemy would make Dragon Ball is an extremely boring series. However, that is not the reason why the Z Fighters do not use this option.
It is true that, without a doubt, Goku, Vegeta and Piccolo It would seem an insult to them to resort to this modality to get out of a complicated challenge. And, if they had the option, they would surely not use it.
But this is also not the reason why the dragon balls are not used to get out of Majin Buu, Freeza or the complicated Cell. The reality is that there is a logical explanation that the series itself tells in the development of its stories.
The first time this was brought up was in the Piccolo Daimaku or Demon King Piccolo arc. There, the good Kamisama he explains that the spheres or Shenlong cannot execute an extinction plan on a being that is more powerful than him.
And how do we know how strong Shenlong is? Well, one similar to that of his creator. With Kami we had some hope, because he was a namek of the warrior race. But with good Dendé there is no chance, since the little green one does not fight even with his worst enemies.
So, this is why the spheres can be asked anything, except to exterminate some villain.