Does setting MTU on logical interfaces affect physical interfaces

From your example, the MTU settings on bond interface need to be as large as largest MTU settings on each VLAN. And I think you don't need to set it on slave eth0,eth1.

from the Red Hat site https://access.redhat.com/solutions/963753:
Issue
jumbo frames needs to be configured in the vlan tagged interface. Adding MTU=9000 in vlan tagged interface i:e ifcfg-ethX.Y or ifcfg-bondX.Y does not help and ifconfig output still shows vlan interface with MTU:1500
Resolution
When one of the VLANs belonging to the interface needs an MTU of 9000 the underlying main non-vlan interface needs to have that same MTU as well. Other VLANs may use a different MTU as per requirement. So along with adding MTU=9000 in ifcfg-ethX.Y / bondX.Y , add it in ifcfg-ethX / bondX as well.
Root Cause
Base interface of VLAN needs to have the required MTU as to propagate changes in VLAN interface.