I am very familiar with both these strings.
For me, it is D'addario Pro-Artes hands down.
For two reasons:
1. The feel.
Aquila nylguts have never felt comfortable to fingerpick. Strum, they are ok, but fingerpicked, they always feel a bit too thin and flimsy to give a solid tone.
The D'addario Pro-Artes feel very comfortable to fingerpick, giving bold, full sounds. I could do a lot more on an ukulele with D'addarios than I can on Aquilas.
Any "audio" comparison of the two strings is 50% irrelevant, because how a strings feel and what they enable the player to do matters more. When you hear a great ukulele performance, very few give credit to the strings. They give credit to the ability of the player and his/her decision to use a certain instrument with a string they chose on it to play the piece that they execute.
2. The sound
Aquila nylguts sound a bit brash and unnatural for my liking.
D'addarios, in my opinion, bring out a fatter, fuller and mellower tone, which I believe brings out more of the unique nuances of the ukulele itself.
If any ukulele I purchase come with Aquila nylguts, I generally end up switching them out nearly right away. Generally my goto strings are D'addario Pro-Artes to replace them.
Obviously no string is perfect for all ukuleles, and at the end of the day, I have to match the strings to the instrument. That being said, more than half my ukes are tuned with D'addario Pro-Arte... none with Aquila (although pretty much all of them originally came with Aquilas when I bought them!)