The CPU chip used on SAM440 does not have PCIe built-in. Some other PowerPC chips do. If they use such a different chip on a future SAM design, then we're in luck. Otherwise they could use a bridge chip to get PCI to PCIe.
Now, the graphics cards are x16 slots, having 16 PCIe lanes. The biggest PCIe port on any SOC PowerPC CPU I know of is x8, such as Freescale's 8641d. AMCC may have one with x8, nto sure, I remember them having some x4s somewhere. Many are x4 or x1. You could still connect and use a graphics card to a smaller port, but you'd only have the performance of the x4 or x1 port it's connected to. I'm perfectly happy with that. I believe AMCC also has PCIe2 on one of their newest chips, which doubles the data rate on a single lane, so their x4 version 2 may be roughly equivalent to Freescales version 1 x8 port, but you need the graphics chip to support PCIeV2 top benefit from that, I think some do this now.
Now, the board vendor needs to decide if it's worth doing that. Do the customers that would keep them in business need or want PCIe? Or would the added cost make the board unattractive to them? The Amiga market today alone isn't going to keep them in business for very long... They may want to give us PCIe slots but cannot make a successful business of it. Or they may have something in design that we just haven't heard about yet.
You could use one of these in a PCI slot to have the equivalent of them putting it on the motherboard:
http://www.semiconductorstore.com/cart/pc/viewPrd.asp?idproduct=5927#details