Many folks remove the crossover assembly, particularly after installing aftermarket springs (which should be your first suspension upgrade - the difference in handling is incredible!) The new springs stiffen up the forks so much that many consider the air option not needed anymore.
But what is the harm in leaving it, especially the older forks with the balancing system? Why Yamaha "upgraded" to individual valves is beyond me. A pain in the ass to get the pressure right, because of the small volume required in each fork, and equally difficult to balance side to side.
I installed Progressive springs years ago, and love the difference. But I also made up my own balancing system, complete with 0 - 20 psi gauge. It's true that the front suspension works well without air, but adding air stiffens the ride even more, making it great for long runs on smooth highways, AND as a control to limit fork diving.
You can eliminate the air system anytime, but why not try the option for awhile to begin with? Just my opinion.
Cheers!