It's a waste of grease, and it would probably raise your temps.
The point of thermal grease is to improve the contact between the IHS on a cpu and the heatspreader on the hsf. The only thing applying paste to the heatpipes would do is insulate them. Which is bad...
depends on where, you *can* see some increase if you have a HSF with heat pipes that are sandwiched between 2 copper blocks as a base by removing the top one, putting a lil bit of thermal paste in then replacing it.