The merchant navy as a career is very challenging in itself irrespective of whether it is for a boy or girl. In the sense that it pays quite well, it is a good job opportunity for those who understand what the job is all about. It is not for the faint hearted and weak willed people. There are few jobs that pay as well. There is no pay disparity in the basis of sex.
The only challenge for the girls comes in the fact that they are still a great minority on board although this is changing slowly but surely.
I've had a few good trainees and junior lady officers, some if them were even better than their male counterparts, and encourage girls to join provided they are ready to brave the adversities that arise. The biggest of these comes from our society (mostly in case of Indian girls) as we as a society have still a long way to grow mentally.
If you don't give a damn to other people's opinions of yourself and believe that you can take whatever comes your way, this is a good field for you.