I would say your roof having a sunroof fitted would be stiffer than one without. However the added weight is where a deficit would come into play.

Structually the roof is mererly a skin on to the structrual areas of the shell.
Other than the higher centre of gravity due to the sunroof framework there will not be any differences noticed IMO.

If you retain the glass sunroof just remove the glass and replace with polycarb.
However if your looking at competing in a race series there maybe complications there with a sunroof model car.