Yes you can use USB 3.0 storage option with Yu Yunique. All USB 3.0 devices comes with USB 2.0 technology as well which will help you use your storage via same OTG cable you were using before. But you will have to compromise with Reading and Writing speed it will not be same as USB 3.0 port.
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YU Yunique has support for microUSB v2.0 & 3.0, USB Host OTG support. So yes officially this device and any other device in future will support the OTG cable. You can read additional support specs on the GSM Arena page.