The commonly stated trade-off for using an anti-alias filter or not is that it diminishes the risk of moire while also reducing potential sharpness. This is what I have seen myself and in many online demos.
Now what surprised me is that DxOMark which measure RAW sensor performance is now split halfway between improvements and setbacks, having tested 4 pairs of cameras with and without anti-alias filter:
95 vs 96 score based on 25.3 vs 25.6 bits of color-depth, 14.4 EV vs 14.3 EV of DR and Low-Light score of 2853 cs 2979. While I expected the D800E to do better in bit-depth, I also expected it to do better in DR.
71 vs 72 score based on only a difference in low-light scores: 889 vs 826.
Both 82 score with bit-depth of 23.8 vs 23.9, identical DR and low light score of 1235 vs 1208. Again I was expected the lack of anti-alias filter to help with DR as well as bit-depth.
The Nikon D5200 vs D7100 do not use the same sensor but results are still surprising considering the D7100 is the newer model:
Score of 83 vs 84 with identical bit-depth, 13.7 vs 13.9 EV of DR and low-light score of 1256 vs 1284.
Thinking about the effects of an anti-alias filter, I would expect bit-depth and DR to be superior without the filter at low ISO when noise is virtually none.
Low-light should be the reverse because the anti-alias filter probably blurs shot noise while read-noise stays the same.
These are my intuition however the results do not correlate. So what is really going on here?
How can the presence or lack of an anti-alias filter explain these measurements?