The CA Shelter in Place and various County Shelter in Place orders carry misdemeanor penalties, however they allow for essential functions and even outdoor exercise to continue. As long as you practice social distancing and do not spend extra time out in public, there is virtually 0% chance you or your ex will be fined/arrested for violating the order while exchanging your son, especially since most of the time will be spent in your car. Regular people are still allowed to "obtain or perform the functions above [https://www.cisa.gov/identifying-critical-infrastructure-during-covid-19], or to otherwise facilitate authorized necessary activities." The point of the order is to allow life to continue while forcing us to be much much more careful to prevent spreading germs.

Courts are government facilities and remain open, though in a reduced capacity. Generally, in custody matters, the court prefers parties who can figure things out themselves. If you can reach an agreement with your ex about where your son will stay throughout the shelter order, that is going to be smoothest and easiest. If you cannot agree, you have the option to file an ex parte application to temporarily modify custody orders, which can result in a hearing and court decision on your question in as little as two days from date of filing. It doesn't make sense to file a request for modification of order, because it will take several months for the order to come down.

Arguably, COVID-19 is an emergent threat to your child's safety. If an ex parte application for temporary custody order is made, a court could rule that it poses "immediate risk of harm" for the child to move about the state, and order the child to remain at a single location, temporarily pausing the custody/visitation aspect of the current order.

To summarize: (1) you can probably continue to exchange your son as normal, (2) it is advisable to reach an agreement with your ex on who your son will stay with, throughout the order, (3) if you do not want to exchange your son or you or your son or your ex (or anyone else in either household) is sick or you cannot make an agreement, an ex parte application for temporary custody order may be necessary.