Yes, you still get PhysX acceleration in SLI, but PhysX can only run on one of the GPUs. SLI on the other hand uses AFR which load balances rendering across both GPUs. The problem is, if PhysX is taking some of the processing time of one of the GPUs, it also reduces the mirrored amount on the 2nd GPU for SLI.
So for example, if you have PhysX consuming 25% of GPU1, that leaves 75% of both GPUx2, so maybe 150% optimally in SLI. If the game only scales to ~150% even without PhysX, you would most likely not notice the difference in FPS overall. If you start increasing the amount dedicated to PhysX, you start reducing the benefit of SLI. Once you eclipse the 50% point for PhysX, you're better off just running them independently, giving a full 100% dedicated to each.
The problem with Batman however is that PhysX on High is very stressful and will use significant GPU resources, probably 50% or more. Its also shown that on High setting, frame rates will generally be limited by your level of PhysX acceleration. So the faster your PhysX processing, the more FPS you'll get before you're GPU limited (similar to a CPU bottleneck).
Here's a pretty good compilation of results for Batman with a bunch of configurations. I also found the game runs better and smoother with SLI disabled, 1 GTX 280 for 3D and 1 GTX 280 for PhysX. Not everyone saw that with 2-way SLI, and there's definitely benefits from SLI + dedicated PhysX.
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