building it into a desk is a bit different from a pc case
is the desk also meant to be functional?
ie--for example your key board and mouse go on top of the desk?
personally if building it in a desk i wouldnt have fans on the top--even with fan guards unless they were very restrictive theres a chance of something falling in the fan if using the desk as a work surface
plus in my opinion fans on the top would probably spoil the look
a desk also isnt like a pc case where in a pc case you could have positive pressure--ie more intake fans than out
because most modern cases have vented areas where the air can also escape
not going to be the case in a desk--so 4 in 4 out may be the best bet