JPipes relies on the structure building system for everything.  The whole wire IO system is completely different so it would require an entire rewrite of jpipes to use it.
Facepunch just added fluid hoses today which replace using jpipes for fluid transfer.  It might be possible to modify the hoses to transfer items aswell but there would be no upgrading or filtering system anymore.

I agree that wires would look a lot better than the low walls but it would come at the cost of losing most of the pipe's features.  I'd like to do it but I'm not going to make any promisses right now.