I don't actually possess a Wyse R90LE but have been sent some photos and information by people who do. (Thank you all).
The LE would appear to be a variant on the L - the added 'E' implying that it provides greater expansion capability. To support this I see that the LE is physically larger than the L being 307mm x 225mm x 82mm (12.1 in. x 8.8 in. x 3.2 in.) in size as opposed to 250mm x 225mm x 53mm (9.8 in. x 8.8 in. x 2.1 in.) of the 'L'. i.e. It's a bit taller and wider. You can see this in the photo above with the extra width providing space for an expansion card to be fitted. The longer back panel is used to add a parallel port.
Shown below are pictures of the L and the LE side-by-side at approximately the same scale. In the case of the 'LE' photo there is riser card fitted to the PCIe expansion socket which slightly obscures the IDE DOM.
Looking at the photos the first obvious difference is in the heatsink arrangement. With the LE there are two heatpipes running to fins located in the extra height of the case. With the 'L' the heat dissipating fins are part of the main heatsink. What's happened here is that the heatsink has been moved to make space for a PCI expansion card to be fitted within the case.
At a quick glance the circuit boards look the same. The main CPU heatsink is located in exactly the same place as are the RAM, Flash, support chips and miscellaneous sockets. However, looking at the bottom left, we see that the LE board in the photo not only isn't fitted with the SATA socket, it is not even tracked for it. I don't know when this particular unit was manufactured, but I have a similar picture from one manufactured in May 2009 (Model R90LE, part # 909535-45L). My R90L (on the right) dates from February 2010. My guess is that photo I've been sent is from the early variant of the Rx0LE (see the Early Hardware tab above).
From the information I have to hand it would appear that Wyse updated the motherboard to add SATA support sometime between July 2009 and February 2010. Unfortunately I don't think there is any outward indication of what you'll find inside other than (possibly) the manufacturing date. It's likely the board update was at the same time that the processor was upgraded to 1.5GHz so that might be another clue.
This is a R90LE from May 2009 which came with a 120GB hard drive fitted (part # 909535-45L).
(Thank you Stephen for the photo).
Here we can see detail from the earlier motherboard. With the later version the area just
above and to the left of the DEBUG BOARD CONN are tracked for a SATA socket.