Does the presence or size of the ferrite bead cylinder on my USB cable affect its performance?
Summary (1)
A properly shielded good USB cable doesn't need a bead and it doesn't do anything in that case.
On a badly shielded USB cables there might be (no guarantees) a reduction in noise that the audio equipment picks up via the bad shielding.
Beads should be placed as close as possible to the connector and ideally at both sides of the cable.
If the connector itself is badly shielded the bead can't really fix that anyway.
Many cheap USB cables are perfectly OK and many very expensive premium brand cables (gold contacts too!) are badly shielded.
(1) Kindly provided by Tonny
It makes very little difference to the performance:
Do the ferrite chokes improve the performance of the cable DATA wise? No. I suspect, as one post stated, that they could tend to round off the corners of the data pulses slightly, but twisted pair technology is very complicated and I don't feel comfortable saying they are actually detrimental.
So what are they there for?
Ferrite chokes are mostly for mitigating negative effects of 2 things: EMI and RFI:
RFI. (Radio Frequency Interference). Any length of an electrical conductor is an antenna in the presence of a radio frequency signal. If you fire up your cell phone, wifi, or 2-way radio next to your USB cable, it is going to pick up the signal and couple it to the devices connected to either end, possibly causing problems. To stop RFI, you need a ferrite choke on BOTH ends of your cable.
EMI. (Electromagnetic Interference). This is electrical noise generated by any digital electronics, and most especially by switching power supplies. (The kind used in almost every electronic device these days that plugs into an AC outlet.) It comes in all sorts of waveshapes and frequencies, and (rarely) can wreak havoc when 2 devices are connected with a wire cable. Sometimes, but rarely, one poorly engineered device can couple so much EMI down a cable that it can actually degrade the performance of the device on the opposite end. You only need one Ferrite choke to block this, and many cables have only one. To be safe, you put one close to each end, which you see a lot of in high end, good quality USB cables.
Generally, the longer the cable the better (worse) it will pick up RF, so these become more important on long (greater than about 6 feet) cables. Also, just having ferrite chokes on a USB cable doesn't mean it is a good cable. One of the most important things is conductor size. Larger wire size, better cable. The trade off is a larger diameter, bulkier cable.
Source: Do USB cables really need ferrite chokes? | AVR Freaks
Are they still needed?
It depends on the quality of the cable you buy. Higher quality cables don't need them as they are protected with shielding. Inside the cable, the copper wire is covered with a special braid and acts as a noise shield.
Note that the connectors must be shielded as well.
In some cheap cables, there is no shield at all. This type of cable is absolutely not compliant and should not be sold under the USB 2.0 name.
...
Often, the cable itself is shielded, but the connectors are not. Sometimes, to pretend, a small wire from the cable shield is soldered to the ground contact, so that a test with a "beeper" provides the impression of a proper shielding. It was such a cable that misled us during our emission tests.
...
Without measuring tools and without references, the only relatively safe way to get a good USB cable in a supermarket is to buy the "luxury" version with gold connectors, often sold for more than $30. All the cables that we tested from this range were properly shielded.
Source: USB cables: shielding matters as well...