How can I be sure that I've plugged a device into a USB 3 port?

You can determine the USB version by running lsusb

• 12M = 12MBit/s = USB1
• 480M = 480MBit/s = USB2
• 5000M = 5000MBit/s = USB3.0 aka USB3.1 gen. 1
• 10000M = 10000MBit/s = USB3.1 gen. 2

Try using something like:

lsusb -D /dev/bus/usb/002/005

The USB 2.00/3.00 corresponds to USB 2.0 / 3.0

Perhaps even try using lsusb -t

The first conversion chart will help you determine the USB version.

Take a look at THIS link for more examples.

My experience is that the lsusb -D command can be a misleading if it reports "capabilities" not currently enabled by the type of jack into which your device is plugged. See below example of filtered output (the entire output of sudo lsusb -D ${USB_DEVICE_PATH} was 80+ lines). In the this example, I deduce bcdUSB 3.00 should imply Device can operate at SuperSpeed (5Gbps) --though that line was still present when I plugged in my drive to a USB 2 jack for comparison.

$ lsusb -D /dev/bus/usb/007/003 | egrep -i 'usb|speed|version|Mbps|gbps|id|speed'

Device: ID 174c:1153 ASMedia Technology Inc. ASM2115 SATA 6Gb/s bridge
  bcdUSB               3.00
  idVendor           0x174c ASMedia Technology Inc.
  idProduct          0x1153 ASM2115 SATA 6Gb/s bridge

  SuperSpeed USB Device Capability:
    wSpeedsSupported   0x000e
      Device can operate at Full Speed (12Mbps)
      Device can operate at High Speed (480Mbps)
      Device can operate at SuperSpeed (5Gbps)
      Lowest fully-functional device speed is Full Speed (12Mbps)

Note also that the idProduct line contained some advisory/marketing text about 6Gb/s which should not be interpreted as an attainable speed.

Alternate short command that might be more useful:

$ sudo lsusb -t | egrep -i "storage" -B1

/:  Bus 07.Port 1: Dev 1, Class=root_hub, Driver=xhci_hcd/2p, 5000M
    |__ Port 1: Dev 3, If 0, Class=Mass Storage, Driver=usb-storage, 5000M