Check what Server Monitor say. It could be too hot so look at the temperature readings. It could be filthy inside, clogged with dust / poor ventilation.
Depending on which fans you are talking about, I expect you can swap them out with an XServe parts kit. Though if the problem is elsewhere such as dodgy thermal sensors ramping up the fans, the problem won't go away.
The level of dust is key to the noise level as the more dust the faster the fans the move and the more noise they make. Also, the fans make more noise over the dust at higher speed.
All the fans in teh Xserve can be replaced. The process is simple and easy. I spead from experiance and will tell you that changing the CPU fan system takes 10 mins for both CPUs.
Thermal sensors are mounted on the mainboard, so replacing those will be very hard.
You can get programs that change the temperature that the sensor thinks it is, but this is risky for a server as it is quite important that you know the actual temperatures of the server.
Let me know which fans and I will point you were to get them from and how to install them.