I want make some rows completely empty so they work as separators. But in rest I would like to keep checkboxes
Instead of storing Boolean.TRUE or Boolean.FALSE in the model you would need to store null.
Then you have two options:
Create a custom renderer that displays the Boolean values normally and recognizes the null value and doesn't display anything.
Override the JTable.getCellRenderer() method. to return the renderer for the Object.class when the value is null. The default renderer for the Oject class will display null as an empty string.