The motor is housed in a plastic container that sits in the cavity so you won't see if the motor is waterlogged. You could remove the inspection panel in the rear wheel well and look inside to see the cavity drain. It will have a rubber one way valve on the end of the drain pipe, pull that off and poke something flexible up the drain to check its free or clear of any debris thats blocking it. If you get water out of it then the motor is probably wet and will need to come out. Threads on here showing how to remove it through the boot and relocate it to the boot to avoid futer water getting into it. Be warned its difficult to get the motor out, its held in by nylon tie wraps inside the cavity and those have to be broken using brute force to free it enough to lift the unit out and back into the boot. If you don't feel brave enough there are guys on here ho do it for a price. Did mine myself took most of the day but knowing how now it wouldn't take as long.
Extract from handbook regarding panel lights
Indicator lamps
> The red indicator lamp will light up while
the convertible top is in motion. It goes
out as soon as the opening or closing
operation has been completed
> If the red indicator lamp flashes after
the button has been released, then the
opening or closing operation has not
yet been completed.
The sequence can be continued in the
desired direction by pressing this button
> If the yellow indicator lamp lights up
continuously with the button pressed,
then the convertible top compartment
panel is raised and the convertible top
cannot be moved.