Yes I agree that there are also hidden place for nuke on WF. However, I still believe it's not balance because
1. Weapon factory roof is big and open area. Yes, it means there will be a lot more spot to place nuke but hotties, patch or mobius can also walk freely on that place and orca can easily kill NOD player if he/she still try to defend his/her nuke. Air strip is disadvantage because that spot is very small area that player can hardly walk and jump, a few c4 from hottie can also do splash damage and kill several technicians, air strip roof also protect GDI soldier from apache. This means that if you are NOD and want to kill WF you have to do many things more than just place nuke and wait, but if you are GDI you can place ion, wait inside the roof, squat and headshot any guys who try to jump.
2. Weapon factory stair is at center of GDI base but air strip has stair at side of NOD base. If you want to place nuke on WF, you have to disarm mine on stair first and it is very hard to do it without enemy's spot. You may do it by SBH but it means you need someone to disarm mine for you because you have not repair gun. For GDI player, it is easier to sneak into air roof because the stair is at side of base and if you are hottie, you can disarm mine and carry ion by yourself. This means that NOD need teamwork to nuke on WF but GDI need only a good sneaker to solo ion air strip (which has higher chance to succeed as I mentioned on first reason).