If the motherboard is mounted vertically, I could see it being an issue. If the motherboard is horizontal probably not.
I use a 1U cooler (designed for a slim rackmount server) on mine. It's comparatively light, as well as very low profile.
The compny I bought mine from no longer exists. Here's a comparable (if not identical) unit: http://www.cwc-group.com/so370lowprco.html