I have some ports on a Catalyst 6509 set to MTU 9216. Some of these ports belong to port channels with a displayed MTU of 1500. I also have a great number of VLANs set to 1500 and not 9216. This is on an aging 6509 chassis with mostly CFCs (though some DFCs) - PFC3A mode running 12.2(33)SXI. What is the negative effect if any of not adjusting the MTUs of the port-channels and SVIs?
Regarding jumbo frame support on the Cat6k, IIRC the default system MTU size is 9216, but there are some modules where a maximum ingress frame size of only 8092 bytes is supported vs 9216 bytes (they'll drop frames larger than 8092 bytes at ingress). Double check the documentation to find out which modules exactly have this limitation.
Regarding the port-channels, if both ports in the port-channel are already set to the same MTU of 9216, it shouldn't make a difference if you configure the port-channel interface to have a 9216 MTU, but it wouldn't hurt for completeness'/clarity's sake in your configuration. You actually can't have two ports in an EtherChannel that have different MTU sizes.
Regarding the SVI's, there's really not much of a difference between routing jumbo frames across a routed L3 interface or an SVI (they're essentially the same thing) - just realize that if fragmentation is required across an L3 interface (ie a jumbo frame is routed from one L3 interface to another with a smaller MTU), the frame is punted to the CPU for fragmentation in software, and this can lead to problems. The rule of thumb here is to keep your jumbo frame traffic localized to other destinations/networks that also support jumbo frames.
While changing the MTU on the VLANs themselves shouldn't really be necessary, make sure that the interface MTU is the same across all the interfaces in the VLAN before setting the VLAN MTU to that same value. And similar to the port-channels, if you already have 9216 as the interface MTU's and the VLAN MTU for those interfaces, it shouldn't actually cause problems to set the MTU of the SVI for those VLANs to 9216.