I picked up a new 34461A and also found the fan noise annoying and wasn't sure about making any modifications. But being new, I suspected there might be quite a bit of drift during its early life so decided to dig further.
The unit came with both the original brief Keysight calibration data plus the full 3rd party calibration data done 1 month later. It was clear the Keysight calibration was an adjustment as all values were perfection, and the 3rd party calibration was a verification as many values were off (yet still within spec). For example, 100 Ohms was 99.9970 Ohms (4-wire, other values were better).
I ran tests with all of my calibrated equipment and unsurprisingly found my old HP 34401A to be a bit better than the new 34461A.
So with that in mind I did not really have any reservations about replacing the fan.
I found the thicker NF-A4X20 5V has higher airflow but lower noise than the NF-A4X10 5V and picked that up. (Do be aware Noctua has 4 versions each of the "NF-A4X20" & "NF-A4X10" and some sellers are sloppy with the specifications.)
The 20mm fan went in just fine and the noise was reduced but still slightly annoying, so I added a trimmer pot to adjust the fan speed lower (a speed controller might be better).
After the modifications, there is still quite a bit of airflow but the noise is nearly inaudible.
Ran through the tests again and could not locate any differences before/after.
So ultimately I would have no concerns with making this modification on a 34461A.
There is no need to cut any wires to install the fan. Simply carefully pull the plastic connector base up through the pins on the PCB with some pliers and connect the new fan directly to the board.