The water pump does not "have to be replaced" but replacing the timing belt is a relatively big job. If the timing belt only took an hour to replace it would be no big deal to ignore replacing the water pump, but seeing as it is a labor intensive job and the timing belt drives the water pump, once the timing belt is removed the water pump is exposed and easy to replace. The timing belt and water pump have lasted say 90,000 miles and the timing belt after replacement should not be due until 180,000 miles. If you don't replace the water pump now you are relying on the water pump lasting until 180,000 miles. If it fails before this time you are duplicating labor to go back in and replace the water pump. It depends if you plan on keeping your Lexus long term (and can financially in these times afford these repairs).
Other items to consider replacing are the timing belt idler, timing belt tensioner, camshaft seals and crankshaft seals. If not replacing them have them carefully inspected.