Hello @vSohill,
Having 1500 on all vmk interfaces and 9000 on the vSwitch + physical switch (or just the physical switch) is fine and won't cause fragmentation - however doing the opposite of this (9000 on the vmk but 1500 on the switch) will of course cause fragmentation.
There generally isn't a significant benefot to using Jumbo frames on vSAN and it adds complexity that can result in issues (e.g. someone lowers the MTU on the switch either intentionally or from non-saved configurations and reboot/upgrade and causes cluster partition).
If it is a requirement to increase MTU to 9000, then configure this on the physical switch (either globally or just the switch-ports in use for vSAN), configure the vDS/vSS to 9000, then schedule a short down-time to configure and validate this on the vmk interfaces.
If the vCenter is running on the vSAN cluster then either set these via the Host UI client or CLI e.g.:
# esxcli network ip interface set -i vmkX -m 9000
Do properly validate that full frame can pass e.g.:
# vmkping vmkX -s 8972 -d <vSAN-IP-of-other-nodes-vmk>
Bob