They do take affect, but maybe not in the way you think. Changes to a species, for instance, changes the template from which new robots are spawned, but it won't change any of the existing bots or their children. So making a bot a veg will mean that only new bots that are created from nothing (say, from a restart or from a veggy respawn) will be veggies and get nrg for free.
All the physics settings, etc. will take affect immediately like you would think they should.