Firstly the diodes D1-D4 are unnecessary. They may even cause problems due to the voltage drop across them. However you should put flyback diodes across the relay coils as explained in the article.I just checked my 60D and the current that flows through the focus and shutter circuits seems to be less than 100uA. So even some small reed relays will do the job.Optoisolators aren't really needed here since the relays are isolating your circuitry from the camera.
I'd defiantly go for a solid state solution, any bounce on mechanical components like a relay could make your camera do strange things.
An optocoupler such as 4n35 is sufficient replacement for your relays. My guess is they are cheaper and less bulky, not to mention silent. They can also be driven by the Arduino board so you don't need 9V (battery ground should be connected to Arduino ground).
Just a practical advice. I would not let the camera focus for each shot because one lens may hunt for focus longer than the other and you most likely won't get simultaneous shots.Set the focus to manual and you need to trigger only the shutter.
I'm also not too sure about connecting the shutter pins together. I'd avoid it, if for no other reason, than just to keep my mind at ease.
I am not familiar with LA-2A Compressor, but an optocoupler is basically a (photo)transistor that (in this case) acts as a switch depending on the state of the LED on the other side. The important part is that the two sides are galvanically isolated from each other meaning the current from one side can not enter the other side (as long as you keep within specs) effectively separating your circuit into two.My Canon DSLR will also focus if shutter pin is grounded (regardless of focus pin) if the lens is in AF, so you might want to put it in MF after all.
No. In MF autofocus is completely disabled.
Why not connect D2 thru a resistor to the camera shutter input?