Have been on loads of tube trips with school children. I have never yet sat - too busy trying to keep an eye on everyone! Some tube trains are a better lay out for getting kids to scrunch up, and also for being able to see / hear what other passengers are saying or need.
Our school policy is to have the children sitting where possible. "Where possible" means if there is a seat and unless there is someone with a greater need. I can easily imagine a child saying they "weren't allowed to get up" especially a younger one. That is broadly the rule, unless we tell them otherwise. We would all usually try to offer a seat if we see someone who might want a seat, but on a long, noisy tube ride it would be very easy to miss someone.
On buses we always go upstairs, so that we are not taking up elderly / disabled seats. I do sit up there, as you get in trouble with the driver if you do not.