Question: "Should more companies be following SpaceX’s lead and not filing patents?"
SpaceX is a unique company, but the way they manage protecting intellectual property rights makes sense.
SpaceX has an ability to protect intellectual property rights through trade secrecy as well as a huge economic moat. Tesla opened their patent portfolio to the public on electric propulsion because it requires the electric vehicle sector to reach a critical mass to make infrastructure a viable alternative to hydrocarbon. Toyota did the same with its hydrogen fuel cell patents. Other companies would be completely inviable without patent protection. Drug companies could not afford to invest in new drugs if they were freely copyable. Whether to patent is completely case-specific.
Patents hinder innovation when the cost to develop is low. Software can fall into this category at times, which is why there is such a heated and live debate over the value of software patents. However, patents serve to spur innovation when the cost to develop is high and the cost to copy is low. It’s a spectrum, so every business will need to consider its own business model in deciding how to go about protecting intellectual property rights.