I can't speak for the D3 but from previous cars I've always done it and seemed to help.
Some good rubber lubricant would be good on the rubber bits and help keep them soft and stop them from cracking.
I need to do mine at some point as well.
Have you tested your drain holes?
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06 3.0TDI Quattro:
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Soft close Doors & Boot, Electric Blinds, Keyless Entry & Start, Bluetooth HandFree, Quad Zone Climate, APS+, 3 Spoke Sports Tiptronic Multi Function Steering Wheel, Heated Seats All Round, Black Leather Comfort Seats, AMI, Sunroof, Drivers & Passenger Electric Memory Seats, Auto Dimming Mirrors, Bi-Xenons AFS2, Dab, Digital TV, Reversing Camera, AV Inputs, Fridge, Solar Roof, TPMS, facelift rear lights, 3G, remote boot closure, Tow Bar.
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