WAV/AIFF are 32 bit formats. the max amount if information that the file formats can store is 2^ 32 bits, or 4 gigs. This means that technically, wav files have a hard limit of 4 gigs. However, most software programs use signed numbers, so they use 1 bit for the sign. This drops the amount of bits available to 2^31, or 2 gigs. So the file format has a 4 gig limit, but most software programs make it a 2 gig limit by using signed numbers.
file systems and operating systems are not the reason for the 2 gig limit. it's a combination of the wav/aiff format and how software handles the files.
To answer the question of "how come a JB3 can split on 3 hours instead of a size issue?" Well, do you know how large a 3 gig 16/44.1 file is? Remember 90 meter dat tapes? They recorded a little over 3 hours, right? What size did it say on there? 2GB.
So it's not a hardware limitation. It's not something hardware manufacturers or software designers decided to make up on their own. It's a limtation in the file format itself. To address larger files, the format needs to be larger than 32 bits. Wav64, for example, although it's not a "standard" (as far as i know), can handle HUGE files, because it's a 64 bit format. 2^64 is a HUGE number of bits