I don't have a PS4 yet to test anything, nor do I follow any PS4 speedrunning communities, but since it's a simple HD upgrade and all games require data install, I don't see a big issue with allowing SSDs (as of now). To me, it's the same thing as buying a PS2 Slim if you own a PS2 Fat just to be faster, or PS3 Fat vs Super Slim. Plus it seems like a huge ordeal to have people prove they're not using their own SSD (I could be wrong on this, no PS4 yet).

I think it makes sense to allow SSDs, at least at first glance, especially since it's possible to install without modifications. The important part, however, would be to sort runs by HDD vs SSD. If there's a huge difference, then it seems like it would be unfair for HDD runners to compete with SSD runners and lose only because of load times. I know PC runs remove loads (which is obviously a lot easier with PC than with console) to make sure that the truly better run is recognized as such, but until 2.8 and 3 come out, it'll be hard to say for sure.

I think it makes sense to allow SSDs, although I would not specifically worry about it until we can get some concrete data on how the timing differs between the two. Of course SSDs will almost certainly be faster, but we may find out after timing that they're only faster by like 2 seconds (or, conversely, by 20 minutes). Let's make it a point to get numbers as soon as we can, but until then, probably not worry too much about it.

Honestly, wait until the Playstation 4.5 since that might be a bigger issue for the future.