Hello CiscoNutt,
interface Vlan1 is an OSI layer 3 interface that is associated to the broadcast domain of Vlan1 ( OSI layer 2).
Trunking is performed at OSI layer 2 and it is not affected by the state of SVI Vlan1 interface you can check this with
show interface type x/y switchport
you will see that native vlan is vlan1 ( Layer2 concept it refers to the broadcast domain not the L3 interface) and the port should be still in operational mode trunking.
Depending on the way the trunk is configured, if DTP is used to negotiate the trunk there is an interaction with VTP, negotiated trunks are not setup in case of VTP domain name mismatch between switches.
If the trunk has been configured manually using switchport mode trunk the dipendence from VTP is removed.
Hope to help
Giuseppe
