According to the documentation, the checkboxes propery is both a getter and a setter. However, when I try to turn off checkboxes, I get an error in my application from jqxcore: jqxcore.js Uncaught Error: Invalid Selector! Please, check whether the used ID or CSS Class name is correct.
Although this error is not thrown in the fiddle you shared, there really seems to be an issue with dynamically turning off the checkboxes of a jqxTree. We have noted this issue and will investigate why it occurs.