the thickness of the strings shouldn't have any influence in and of itself, as there are two main factors in latency - the pitch of the note, and therefor the length of time it takes for one complete cycle to take place to be read by the convertor (or with the Axon and Yamaha systems, half a cycle). the other factor is the amount of unreadable noise on the front end of the note, and this is more a factor of right hand technique and set up than anything else. Things that are unreadable include the sound of your finger scraping over the string, fretbuzz, any thudding percussive sounds etc...
so clean technique is going to be the deciding factor so long as the strings are tuned to the same pitch...
steve
www.stevelawson.net