When checking the attached output, it looks like all Shelves running with 3Gb/s Link speed. If mixing shelves with IOM6 and IOM3 in one Stack, the link speed gets throttled on all shelves in this stack to 3 Gb/s.
Because of that, if performance is a factor, shelves with different link speeds should be separated in different stacks.
Also keep in mind, that there should be only one conversion between shelf modules, so prevent a configuration like: IOM6->IOM3->IOM6 and daisy-chain the new DS2246 shelves to the DS4246.
There is also a statement about this in the Storage Subsystem FAQ: