It seems to me that under Cisco IOS-XE (switches at least - I’ve experienced this on Cat 4500-X and 9500 platforms) VLANs on trunk ports are not discovered. Only VLANs that are set as the native VLAN for a trunk, or on access ports, are detected.
I guess this is probably because previous (non-XE) IOS versions supported the Q-BRIDGE-MIB properly and had the tagged VLAN assignments in the dot1qVlanCurrentTable (so covered by the code in q-bridge-mib.inc.php), whereas IOS-XE does not. Instead that information is in the CISCO-VTP-MIB vlanTrunkPortTable (vlanTrunkPortVlansEnabled specifically) but the code in the vendor-specific cisco-vtp.inc.php does not read that and instead only deals with the native VLANs.
This is probably the same issue posted in Cisco ISR1k & ISR4k routers monitored not showing correct assigned vlan on switchports that did not get an answer.
I may get around to trying to patch that myself, but someone familiar with the VTP or Q-BRIDGE-MIB VLAN code might do a better job. This has got to be an issue for a fair few people; IOS-XE is popular these days surely?