Not necessarily.
There is a list of formats that the kindle supports in the Kindle Device Driver under Preferences->Plugins->Device Interface Plugins that is arranged in priority order, and if the format is on the list then it could be sent. If you have both mobi and azw enabled then whichever believe is higher up the list and would thus be sent in preference.
I believe that by default azw has the higher priority so you would want to change this and move mobi up above azw. However if there is no mobi format file then a lower priority format could be sent, so you should disable any formats you do not want sent.
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