Yes, there are plenty of motorcycles that came stock with a magneto system although most of these motorcycles would be considered vintage bikes. One example is the Harley-Davidson Sportster
XLCH, generally considered a 'Competition Hot' model. XLCH Sportsters came stock with a magneto, while the standard XL and XLH models were equipped with a battery and points ignition. Pre-1963 Triumph motorcycles
, such as the T120 Bonneville, T110 and others also had a Lucas Magneto ignition as stock.
There are still many new dirt bikes that use a magneto system. A good sign that the bike may have a magneto is if the bike has a kick start lever. If you see a kick start lever, there is a good chance the bike has a magneto.