I think malware and viruses are less common for many reasons, but I suspect increased awareness and security posture (including the architecture of modern OS) has more to do with this than "walled gardens." Malware does make it onto closed app stores, and many users (e.g. on Windows) still don't use app stores.

The answer you're looking for is probably to build more decentralized, FOSS software with better UX. Much easier said than done of course.