I've been out in mine this morning and tried to pay attention to the noises prior to starting the engine. There is a small whirr which seems to be the fuel pump priming as per my earlier post, then nothing until the starter is operated.
Opening and closing the hood seems to provide a much more mechanical noise both from the hood motor and the mechanism itself, this is a different noise from the fuel pump but there is no noise from the hood motor until the button is depressed to commence the hood operation. On closing the hood, mine slows as it approaches the screen header rail and does shut with a bit of a thud prior to the latches engaging. I have never viewed this as anything other than 'normal', the process is fairly smooth but appreciate this term may be very subjective. I would imagine if there was a problem with the motor not providing enough hydraulic pressure to operate the roof mechanism, it would not open or close fully, likewise if the motor was failing from water ingress. I cleaned the drains when I first got the car and it is something I will continue to do on a regular basis having seen comments on the forum about the fragility of this part, but as I have said I have no noise from the hood motor on position 1 or 2 of the ignition switch or indeed start up, until the button is operated.
Sorry this is so long winded, but hope it is of some assistance.