Facing upwards the fan would be fighting the GPU for air!
not really, ive done several antec 300 and 900 builds. I always installed the PSU fan side up, in fact I run the PSU fan side up in my corsair 400R. The real issue is dust so I always used a fan filter.
as far as effecting cooling, I've run stress tests using my corsair & antec PSUs in my corsair case with PSU fan side up and down. All temps where identical. Good cooling starts with a good cooler on the chip and proper case airflow.