Supporting jumbo Ethernet, I believe, only slightly increases possible MTU related issues. Why? Because hosts that support jumbo Ethernet can try to transmit jumbo sized frames on switches not supporting jumbo. With jumbo support, the jumbo frame gets a bit further.
The difference are (with jumbo enabled), a host might receive (in the same L2 domain) a jumbo frame it cannot support. If so, it should reject the frame. Again, remember, if jumbo wasn't enabled, the host shouldn't have gotten the frame at all, so other than consuming bandwidth to the host, the net effect is the same.
Additionally a host might receive multiple frames, from a jumbo frame whose packet was fragmented at a L3 hop. The biggest problem here, often is the network device that needs to fragment the jumbo frame, which may increase the CPU load on that device. Otherwise, not much of a difference beyond if a fragment packet is lost, the whole jumbo frame will need to be resent, rather then a single frame/packet which was not fragmented.
A sometimes overlooked issue when using jumbo Ethernet is, there is no standard for jumbo Ethernet. So, you can sometimes run into jumbo MTU issues because different devices might have different jumbo MTUs which can lead to MTU issues.
Personally, because there's no standard for jumbo Ethernet, I advise to stay away from it (yea, I know, storage folk want it - but, I think, mostly because they can - it's not quite the panacea they tout).
One of the biggest benefits to jumbo Ethernet, is you're able to raise the percentage of data being transmitted (see Ethernet bandwidth efficiency ). It also decreases the processing overhead, of processing frames and/or packets (as there are fewer for the same data volume). Again, though, are these benefits, so necessary, to use something non-standard?
