In general you ALWAYS need some fans to ventilate your case, and of course some fan (or other system) to cool the CPU. Your story suggests a couple of ideas.
First, if the fans always were noisy from the beginning, it is entirely possible they were always running full speed. This can happen if they were connected directly to the PSU for power (which has no way to control speed), rather than to mobo headers. It can happen if the fans are connected to a case-mounted fan speed system with a manual speed button, and you never chose to change the speeds. It also can happen even if they are plugged into mobo headers, but the header(s) they use either are configured for constant full speed, or are set to use the new PWM Mode of control even though the fans themselves are the older 3-pin design. In any of those situations, some adjustments to the system could reduce fan speed and noise.
Secondly, if you now have NO noise as a result of a recent change, and your HWMonitor tool says all the fans have ZERO speed, that's a big warning. Now, zero speeds could happen simply because the fans never were connected to any mobo header and the mobo had no speed signal to show you. But it also can happen if the fans ARE on mobo headers and HAVE failed. If that is the situation. you really do need to replace them, and MAYBE change the way they are connected and controlled. For this, you need to open your case with the power off and look inside to locate the fans. Then turn on your machine and observe the fans immediately. The NORMAL sequence is that every one of your case fans should start up right away at full speed. After a few seconds, they all should then reduce their speed to whatever is needed for a cool system, but NOT stall. Thereafter as you use it, the fans should change their speeds at higher workloads. If you do not see all of that, tell us exactly what you do see.
If you need advice on how to change, tell us these details:
What maker and exact model number is your mobo?
How many case ventilation fans do you have?
If you can, tell us the maker and model number of the fans (usually on lables on the hub). If that's not clear, tell us what the label does say in terms of Volts, Watts, and / or Amps. ALSO tell us how many wires are in the cable from the motor, and how many holes are there in the connector on the cable end?