I am not at all an expert on ZnO (I am familiar with a bunch of other oxides), but a quick google Scholar search suggest that most people who try to grow epitaxial ZnO do so on R-cut sapphire and/or use a buffer to allow them to grow it on Si. Hence, any articles you've found where they grow ZnO directly on Si probably describes work where they don't need the ZnO to be epitaxial, in which case you can use (nearly) whatever substrate you want; in which case the reasons I outlined above come into play.
Also, note that there isn't in practice that many substrates to choose from. There is of course a bewildering number of material that could potentially be used a a substrate, but only a handful or so are available as high-quality reasonably large wafers (say larger than 5x5mm2). This is another reason why most people -regardless of what they are studying- end up using Si or sapphire.
To answer your second question: I would be very surprised of ZnO diffused into Si. AFAIK this only happens with certain metals (most notably gold). I would also be surprised if SI would break down, this would only happen at temperatures way higher than what would be used in any fabrication method I've ever encountered.