The GPU die including the HBM modules are under a common IHS, so I expect a flat surface on that IHS. But anyways, there will be waterblocks nevertheless. Trust me.
I'm quite sure you'll find waterblocks for the 390X soon after it's released. I'm just not sure about the IHS. To the best of my knowledge, AMD never used an IHS for any of its GPUs (not 100% sure about ATi, but my memory says no) and I don't think they will this time either. Since those HBM chips are almost certainly taller than the GPU die, using an IHS only makes sense if they'd need to protect them from damage (as in, due to the fact that they are stacked, the chips would break under the pressure exerted by the cooler's retention system). Even so, there are far more elegant and more efficient methods to handle this than a full-blown IHS.
Not to mention that using an IHS, combined with the taller HBM chips, would lead to a pretty thick layer of metal right above the GPU die, and that would lower the efficiency of the entire cooling setup. This leads me to believe that either there won't be an IHS at all (they are likely to use a "frame" like they've always used for high-end GPUs) OR they'll use a very atypical IHS (one that has "bumps" right above the location of the HBM chips, so not a flat surface at all). Either way, ye olde "conventional" waterblocks won't work here, you'll just have to buy a new one or modify the base of an existing one to fit the bill.
Also, the sheer size of the GPU package (certainly much larger than that of any GPU released to date, at the very least the size of an LGA2011 CPU package) leads to other complications. First and foremost, the holes for the cooler's retention system are going to be spaced much further apart. This would result in something more along the lines of what you typically see on a motherboard rather than a graphics card as far as said holes are concerned. This also leads to my second point here, which is that the 390X's cooling system (stock or custom) is extremely likely to employ some form of backplate to prevent the PCB from warping too far and breaking the BGA contacts or other parts (such as the dies, but not only). There are a couple of viable options here: either a system that pretty much works the same way as that on the AM2/AM3/AM3+ sockets, or a metallic X-shaped spring system (which is more commonly used for graphics cards, think about the HD 4870/4870X2, for example).
Either way, whatever's hiding under the cooling system of the 390X is unlike just about any graphics card you've seen to date.
