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If the 'Send Transactions Via' Email checkbox is set on the Customer &gt; Preferences does this mean that when a Sales Order is created an email will be sent out?

That will default the email checkbox  to set on the transaction. It’s the transaction checkbox which will send the email. I say this as it’s possible users toggle the transaction box which overrides that customer default. 

Right, that's what I thought was happening. I tried creating a WF to ensure the To Be Emailed on the SO is always unchecked, but my WF hasn't yet worked.

and are you sure there isn't something else sending the email, like a script or workflow?

that being unchecked on the customer has always worked for me.

By default we have the email checked on the customer record. There are some orders which are generated by a bundle we have, and need those to not send emails out. My WF seems ok when editing an existing order, but for new orders it doesn't get triggered.