Roof rack systems will normally work with sun roofs without problems. However your specific 2000 Lexus LS400 presents issues with all the major car rack manufacturers (Inno Racks, Thule Racks and Yakima Racks) for a typical roof rack system. Nothing is compatible. However there are some alternatives such as the Malone HandiRack inflatable roof rack system and the SteelCore Soft Rack-Travel Rack. These are great solutions for carrying ski-snowboard bags as well as all kinds of other items including a kayak, surfboards, luggage, lumber etc. They also make great rental car roof racks when you need a temporary car rack solution when renting a car.
Malone HandiRack inflatable roof rack system
http://www.orsracksdirect.com/malone-handirack-inflatable-roof-rack-mpg452.html
SteelCore Soft Rack-Travel Rack locking roof rack system
http://www.orsracksdirect.com/steelcore-soft-rack-travel-rack.html