How Nova's powers work has always been kind of vague in the comics. Probably so writers aren't limited in how to use them.
It seems that Nova powers (the Nova Force) are based on manipulating gravimetric forces. His strength and invulnerability can be explained by Nova making things lighter to him by taking away gravity from it and using gravity to repel things hurled at his body.
His flying abilities were explained a long time ago as that Nova flies on electron paths.
I hope that helps. It looks like Nova #31 may give us some more answers on how things work.
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