We have tested our device for EMI without extenal chokes. We are able to pass FCC class B limits without the chockes.But there are devices in the market for USB 3.0 EMI filtering such as DLP11TB800UL2 from Murata.
For ESD there are many devices in the market that does not severly impact the 5Gbps USB signals. Little Fuse (SP3010-04UTG) and Amazing Devices (AZ1065) have devices with low capacitance (.05pF) that can be used for this application.
Our company (Inpaq Technology) offers both ESD and EMI solution for USB 3.0. TCF0504U500 is a good EMI filtering choke for USB 3.0 and TVU1206 is a ESD component with very low capacitance which keeps good signal performance in USB 3.0.