I would think the reason you don't see many chokes trained in aikido is that it is really complicated and imho somewhat unrealistic to position, lock-in, and finish a standing choke.
If you look at most arts that use chokes heavily you will see they are done on the ground. Without a large grappling portion of training, you would be better to skip chokes.
I understand the reasoning here, but I disagree... shimewaza when done properly can be done standing, from all four directions. Success is dependent, as all waza should be in my opinion, on properly applied kuzushi principles, taking the sente and keeping it.
After thought... of course, this really comes down to what brand of aiki practice you're training in and what their practice methods are like. Nothing disparaging intended, by the way... just different strokes for different folks.