Solution
Yes, jumbo frames are supported in CompactRIO-903x.
Once, you plug in GigE Vision camera to one of the Ethernet port of CompactRIO, a dialog pops up asking if you want to enable jumbo frames.
If you click "yes" on this dialog, jumbo frames are enabled and the setting is saved in the INI file, "/etc/natinst/share/ni-rt.ini". The line, mtu="9000", is added under [eth1] section and jumbo frames are enabled.

You can also enable jumbo frames programmatically on cRIO with SSH.
Follow
this link to access the shell of NI Linux cRIO.
Type
ifconfig to check the configuration of the Ethernet ports. The default MTU(maximum transmission unit) of ports should be 1500.

In order to enable jumbo frames, change this value to a higher value such as 9000 by typing
ifconfig eth1 mtu 9000. This will enable jumbo frames on the second Ethernet port.
Verify that the change has been made to the port by the command
ifconfig.
This command changes jumbo frames setting temporarily. Restarting the cRIO will return MTU values to default.