With Cisco Enterprise kit the management plane is used to intiate connections into the device and control it. It can often bve unecrypted using telnet and SNMP v1 or v2c. Also anyone having dirtect access can attempt a DOS attack and prevent you getting into your own kit.
So there is some good reason to protect this.
Meraki kit uses an encrypted outbound stream to the Meraki cloud. So I don't personally bother with a seperate management network. You can also disable the Meraki local status page to further protection.
The only special exception you could consider is when using SSIDs with WPA2-Enterprise mode. However a feature was recently added to allow RADIUS traffic to be sent over a seperate VLAN.
Personally I tend to use the one VLAN.
Changing the native VLAN is mostly related to preventing VLAN hopping attacks. If this is of a concern you should use a different native VLAN on trunk ports between switches. For safety, this should be a VLAN not in use in the network. You want every valid VLAN to be tagged between switches.
You don't really need to use it in other places.
Personally, I wouldn't worry about it.