Your mileage may vary, however, in my experience and that of many others, side fans are certainly not a waste of time when set up correctly.
ED: So directly removing the hot air that's being vented from the gpu's out of the side of the case hurts airflow and can make cpu temps rise?
That's strange, you would have thought that allowing that hot air to rise inside the case and be fed to the cpu cooler would have that effect instead.
As for getting better intake fans, there's sod all you can do to improve the front airflow in a Shinobi apart from cutting out the grills which doesn't do a hell of a lot except lower noise. Other than that, dremelling a big hole in the front panel or removing it completely is all you can do, and that's not really on the cards.
LtMatt has the same case as you, Murah. He also found that using side exhausts lowered gpu temps when he was using an Accelero, and side intakes lowered gpu temps when using IceQ xfire rear venting cards.