45 W per channel would be 45/12=3.75 amps, however I got to warn you if your running at max draw your going to be running into problems of a different sort, you'll be creating heat!
Also I assume this controller uses some sort of digital PWM to control the fans and yes that can cause a whine if it's not properly capacitor'ed at the output. ( properly sized capacitor and a diode to prevent chargebacks into the controller is a must for any fan controller that wants to avoid the whine factor. Zahlman fan controllers used a method that created alot of heat but avoided the whine (this was the first commercial single fan controller) that allowed tach signal pass through.
the start-up factor could also be alleviated by using a smoothing capacitor. however if 45W is the max per channel you should use no more than about half of that for daily use (i.e. no more than 4 fans per channel and that is pushing it)
the problem with fan controllers is that they tend to design them to spec, to save money hence they usually dun spend the extra money for a good really oversize smoothing cap.
so some noise tends to get through.
just one question though WTF do you need 18 fans I'm right now designing a new case and it will have 5 fans 3 in the water cooling compartment, two in the main board compartment.
there comes a time when more fans are overkill.
Directed airflow would get you better results.
well good luck
terramir