The aquaero 4.00 works with analog voltage regulators. Only the really old version 3.07 was using PWM but also only with 3-pin connectors. Normally every PWM fan should work on a regular 3-pin connector since the 4th pin is only optional for the PWM function. If you don't know it so far: PWM means no real voltage regulation and is something that you should avoid.
I don't understand your question with the aquaero and aquabus. There is no way to connect the aquaeros via aquabus. The only way to communicate is USB or you do everything directly through the buttons and display.
You can connect hundreds of multiswitches to the PC. Every USB device gets its own tab within the aquasuite.