He just said he can't afford it regardless of that.
You can easily suppose that having Nadal wear the watch is more valuable to them than the watch itself. Think about it: Wilson took the plane from Chicago to Switzerland (or wherever Federer was at that time) to make him try new racquets and customise them between training sessions. Surely that seems a bit excessive right? Well not at all: Federer is worth a lot more to Wilson than the racquets they give him or than a plane trip to Switzerland, a pack of lead tape and a bottle of silicone. Federer brings them much, much more money and recognition than he costs them.
That's really the gist of sponsorships: it's a relationship between you and a company. Both of you must be getting something out of it. And for a company to give you discounted or even free stuff, you must be more valuable to them than the cost of the stuff they give to you. Same when a player gets paid to appear at a specific tournament. Now, if Nadal was losing a lot of watches, RM would most likely become suspicious, but it doesn't seem to be the case.