Zitat

I am building a 2x water loop system, so I need to connect 2x Aquacomputer D5 usb/aquabus pumps to the AQ6 xt controller. I want to control both pumps independently of each other. I've researched and foundthat this can be done, via a splitter, which allows me to assign different IDs to each pump and therefore control them independently. This is still true, correct?

Yes.
You can assign an ID number to the pump using a USB connection and the aquasuite software.
The aquabus connection is not required to do this.
The ID is set in flash memory, and will stay assigned even if all connections to the pump are removed.

Zitat

Also, I understand that I only need a 3 pin cable (regular fan cable will work) since the pumps have a separate powersupply, via the psu. However, will the 4 pin cable be a better option? If so,
why?

The 4 pin cable is not a better option for the USB/aquabus pumps, but they are also not a hindrance... the 4th wire is simply ignored.
The positive part of a 4 pin aquabus cable is they are never wrong for an aquabus connection, a 3 pin aquabus cable may be wrong for some aqaubus devices (i.e.MPS flow &/or pressure sensors).

Zitat

Aquabus pump setup question:

According to the manual, I need to connect the USB cable tothe MB and connect the aquabus cable (3 or 4 pin) to the controller in order to
setup/create IDs for the pumps, after which, I can then remove the USB cable(I'd like to keep my usb headers free for future use).

1. Is it best to set up one pump at a time using this method? What is the best method to do the setup?
2. Can I connect a 4 pin cable even if the psu is providing power to the pump? Will this cause any
adverse reaction?

As I mentioned above, you do not need the pumps to be connected via aquabus to set the ID... you can actually set the ID's using another computer (laptop) if you wish.
And yes, once the ID is set you can remove the USB connection.

1. You can do one at a time or both, doesn't matter.
The only part I don't remember, is if the PSU connection needs to be connected to set the ID, I believe not.
Someone will correct me if the PSU connection is required.

2. Yes, you can use a 4 pin cable. I use only 4 pin cables so I do not have to concern myself if the module needs a 3 or 4 pin cable.

Looks like you did some serious research. Congratulations