It all depends on whether the heat has anywhere to escape efficiently. An amp is designed so that heat can rise up out of it. If it's on it's side, the casing may not have any facilities for this to happen at the side, plus, heat from one side of the amp (bottom) will be passing up past the rest of the circuitry, heating it more so.
The quality won't be affected. You could try it, but check to see if the amp gets hotter than normal at the top (side). If it does, I'd not recommend it.