Mine is the same. I notice it's less groany if it has been raining (why?)
Car is full of rubber bushes / bearing parts - could be any (or several) of them.
Obvious step is to go right round the car & do all the doors / roof mechanism sections / boot / bonnet with silicone grease - may or may not sort it. Then you are onto the dirty bits under the car. Not just the rubber gaskets - do the bump stops for bonnet & boot too.
Convertibles are nowhere near as rigid as a hard roof car & they absolutely do flex / twist over the bumps, especially if you are at an angle.
I 100% would not recommend going over a bump with the bonnet raised - it's way heavier than you think, and you might twist the mounting points / damage it horribly.