I would put filtered intakes to the sides of the bottom chamber. Not because of what you brought up, but because you're going to get a lot of airflow through that hole in the rear, and the smaller the hole, the faster the air will flow through it... and if you don't design the intake well it might start to make turbulence and noise when the pressure differential created by the fans grows big enough (ie. the amount of air they suck in). Depends of the fan capacity as well, of course. I don't think the airflow of the later fans will be meaningfully hampered by the location of the intake hole in this kind of scale, unless you're planning on putting in some jet compressor fans or something. There will be some effect, but how much is a different thing.
Actually what happens is that each fan creates the same pressure differential between the "up" and "down" side of it. If the chamber below is sealed, this will move some air from the lower chamber into upper, and then the fans will work to retain the pressure differential between chambers. If you open the back of the chamber, the pressure differential will start to evan out starting from the rear, and instead of a pressure differential there will be an airflow from the lower chamber to upper chamber. But, because the fans at the back are further from the intake, the air can't get to them as easily as the first ones, so the air pressure in the chamber will reduce the further you get from the intake, and that will slightly reduce the amount of air available for the last fans to transfer, but at the pressure differentials and air transfer volumes that PC fans are capable... I don't think that's the thing you need to concentrate on. Building bigger intakes to the sides is a better solution for other reasons IMO; it would just take care of that potential issue as well.
Making a bigger hole for the air to flow will reduce that (and as a bonus it will pretty much ensure equal airflow for each fan).
Also, think what happens when you place the HD tray above the last fan full of stuff. Same with optical drive location, actually. And all the horizontally placed extension cards like GPU's and sound cards and network interface cards and other stuff. Does the case really need that much fans, and is the vertical airflow really the ideal solution here?
Also... as far as I can see, it would be good to have an equal amount of intake and output fans, at least roughly. If you have more intake fans than outtake fans you'll create an overpressure inside the case and air will start bleeding out from each seam and hole available to it, and you lose some energy to maintaining the overpressure, and you don't get as much control over the airflow... In this case that might not be an issue though, since your case has almost open upside, but in more "sealed" cases it is worth thinking about.
Nota bene: I have no experience building PC cases, but I do have some insight into physics and, by extension, fluid dynamics...