Will it affect also tunnels/openvpn/wireguard/vxlan etc?
If you get rid of the default MTU values you get more pain.

I have no proof now of any obvious negative issues. Moreover, in my personal opinion - if some protocol or interface type requires a default MTU that is not assigned to it by the kernel, this is the problem that should be solved by configuration script for that particular interface.

Forcibly stretching the same MTU to all interfaces, regardless of other system components' logic, does not seems to be a good idea as well as missing default MTU for interfaces that may require it. Here I think that easier to assign MTU where this is really necessary than ignore it where it interferes with something.

Will it work if you replace this https://github.com/vyos/vyos-1x/blob/4168e03721b2a9595de4090fddf1280d39ccce4c/python/vyos/ifconfig/interface.py#L1378-L1379

sudo nano -c +1385 /usr/lib/python3/dist-packages/vyos/ifconfig/interface.py

with:

# MTU - Maximum Transfer Unit
#if 'mtu' in config:
#    self.set_mtu(config.get('mtu'))
if 'mtu' in config and 'dhcp' not in new_addr:
    self.set_mtu(config.get('mtu'))

To solve the issue with MTU over DHCP we can use some new options like mtu for example:

set interfaces ethernet eth0 dhcp-options mtu

PR https://github.com/vyos/vyos-1x/pull/1452

PR for 1.3 https://github.com/vyos/vyos-1x/pull/1453