Local minima traps are a much discussed and widely experienced issue. I would say it is an active area of research, and hence there are differing views. Some claim there are no traps in an unconstrained optimisation (see work by H Rabitz group), but one has to consider that constraint covers lots of things, e.g. pulse amplitude limits, timeslot size, total energy available. I have found, in my reasonably limited personal experience, that as I increase the degrees of freedom more traps occur. How to avoid, counter, or escape, local traps is still much under discussion. The CRAB people in Ulm claim to have a partial solution using the latest version of their algorithm call adaptive CRAB. I believe there is published work on this too now. I know that they were/are working on extending qutip to include this method.
The blunt instrument used by most people is to run many optimisations based on different initial conditions and choose the solution with the best fidelity. Of course this does not mean that you have a global minima. Finding the global minima is literally a hard problem.
I would say that there is no reason to believe that the standard CRAB algorithm is less likely to fall in unwanted local minima. There are many reasons to use the CRAB algorithm. These are mainly around when you want a pulse that is more easily physically realised. Nelder-mead is considered to be the best method when you can't calculate the fidelity gradient with respect to your pulse parameters. If you can, then a gradient based algorithm usually converges faster. However, as mentioned previously, adaptive CRAB may help, but I have not tried it personally (yet).
I would say that 10 seconds per iteration seems very efficient for a system of the size you mention. This is very interesting.