I believe both the C9300 and C3850, by default, have QoS enabled. However, enabling AutoQoS, I also believe, changes QoS parameter settings.
Unsure about the Nexus 9K. I recall (?) other Nexus switches did not enable QoS by default.
Whether QoS is running using a device default, or using AutoQoS, neither guarantees their QoS is truly suitable for your needs. (Both, though, generally will "better" handle most real-time traffic vs. disabled QoS.)
"What are the best ways to troubleshoot QoS?"
Depends on why you think QoS needs troubleshooting.
You mention VoIP audio quality issues. Problems across all devices, or just some devices? Problem during anytime of day, or just during prime business hours?
CUCM provide stats? (I'm not a VoIP engineer, although I have much experience supporting various traffic types, including VoIP, using a network.)
"Some ports are not configured with 'auto qos trust dscp, . . ."
That could be a problem, if VoIP packets are having their ToS tag not honored.
Unfortunately, there's so much with QoS that might be done "wrong", your question is like asking "we think we have a network problem, how do we troubleshoot it?"
