Two Leonardos on one USB hub - not working properly
There is no reason I can think of that would stop it working as it should.

lsusb is showing both the devices, so they are being detected by the kernel.

You can try running usb-devices from the usbutils package (should be already installed since lsusb is in the same package) and look for the two Leonardo blocks. You should get two blocks like this:

T:  Bus=01 Lev=03 Prnt=07 Port=00 Cnt=01 Dev#= 11 Spd=12  MxCh= 0
D:  Ver= 2.00 Cls=00(&gt;ifc ) Sub=00 Prot=00 MxPS=64 #Cfgs=  1
P:  Vendor=2341 ProdID=0036 Rev=01.00
S:  Manufacturer=Arduino LLC
S:  Product=USB IO Board    
C:  #Ifs= 3 Cfg#= 1 Atr=80 MxPwr=500mA
I:  If#= 0 Alt= 0 #EPs= 1 Cls=02(commc) Sub=02 Prot=00 Driver=cdc_acm
I:  If#= 1 Alt= 0 #EPs= 2 Cls=0a(data ) Sub=00 Prot=00 Driver=cdc_acm
I:  If#= 2 Alt= 0 #EPs= 1 Cls=03(HID  ) Sub=00 Prot=00 Driver=usbhid


The important bit is the I: lines - they show the individual USB interfaces and what kernel driver has been associated with them.   For the keyboard, of course, it's the last entry, which is assigned to the usbhid driver.

Another good diagnostic is dmesg -w

Run that with both Leonardos disconnected.  Plug one in and it should show it registering as a USB device.  A few moments later you should get a pair of lines like:

[ 2106.937086] input: Arduino LLC USB IO Board     as /devices/pci0000:00/0000:00:1a.7/usb1/1-1/1-1.4/1-1.4.1/1-1.4.1:1.2/0003:2341:0036.0006/input/input21
[ 2106.990523] hid-generic 0003:2341:0036.0006: input,hidraw4: USB HID v1.01 Mouse [Arduino LLC USB IO Board    ] on usb-0000:00:1a.7-1.4.1/input2


That is the board being associated with an input device (in this case input 2).

Repeat it with the second Leonardo and see if the same appears, but this time with a higher input number (it would be 3 on mine if I had a second Leonardo).

The fact that the two Leonardos work together normally means that they should be working fine in any arrangement, so if the OS is seeing it all fine but the data isn't getting through, then my money is on the hub.  It looks quite a new hub, so it may have a few bugs in it that are yet to be ironed out.

USB devices are identified to the drivers using the VID and PID, but to the kernel the USB device is just a chain of bus/port numbers.  For instance my Leonardo above is identified as:

1-1.4.1


That's USB bus 1, downstream port 1 (root hub - normally only has 1 port), which connects to a hub (the one built into the computer to drive multiple ports) which then has downstream port 4 connecting to a hub (on my desk) which then has downstream port 1 connecting to the device.  Nothing else can be connected to that same combination of downstream ports - it's physically impossible, so it's uniquely identified.