Hello I ask the same to my trainer he told me that those protocols will still use vlan 1 to send their data.
I found a deeper explanation on the book "Cisco LAN Switching Fundamentals: Configuring Switches"
Here is an extract
"It is important to remember that even when VLAN 1 is cleared from a trunk,
the previously mentioned special traffic, such as CDP, PAgP, and VTP, is still
forwarded across the trunk with a VLAN 1 tag, but no user data is sent using
VLAN 1. All trunks default to a native VLAN of 1 unless changed. In the case of
an 802.1q trunk, where the native VLAN is untagged, 802.1q IEEE Bridge Protocol
Data Units (BPDUs) are forwarded untagged on the common spanning-tree VLAN 1 for
interoperability with other vendors, unless VLAN 1 has been cleared from the
trunk. Cisco Per-VLAN Spanning Tree (PVST+) BPDUs are sent and tagged for all
Just want to clariry that special traffic (CDP, VTP, STP, PAgP etc) will always be sent across a trunk link either tagged as VLAN1 or untagged when VLAN is the native VLAN. So effectively (to my understanding) VLAN 1 is ALWAYS the management VLAN. This is because VLAN 1 can NEVER be removed/deleted etc.
This is a interesting discussion as I was actually asking myself the same question the other evening when reading up on this. So, if I setup ALL my switches and trunk ports on my switched network to use the default VLAN of 99, will i see my BPDUs and CDP all tagged with VLAN99 or untagged?
There is also another interesting discussion on these forums here;