The deeper the trance, the strongest the effects of meditation and witchcraft. Trance while doing a physical activity is a very advanced ability which I suppose needs the kundalini risen or analogous levels of development. You should do it when you are still. For cleaning your aura, there are asanas to do that if you want to do it while moving. By virtue of those Qigong movements, you can clean your aura. Not by simply walking and half-assing JoS meditations.
I used to everything with my eyes open and I did it for several years. The thing is that the depth of the trance when your eyes are open is not the same, but it's less deep even if your body is still. Does it work? Surely it does. However, experience shows it is less powerful and thus less effective. In my case, doing everything with eyes open means operating at 10%.
Void meditation is a very basic meditation and the foundation of all meditations. All meditation is in fact a variation of void meditation, with the focus as the object of the meditation. The stronger the focus, the stronger the effects. Same for witchcraft.
Comfort is not a factor here. Or, to say it better, it is normal for some people (like me earlier on) to feel uncomfortable with their eyes closed. In my case, it was fear of sensory deprivation and in general "restriction". So, discomfort/anxiety would build up but I was well-advised, when I got an astrology reading several years ago and asked for clarification, to push past that feeling. When you push past that feeling, you'll experience all the power and intensity you've been missing on.
Ultimately, it is about you and your goals. What are you trying to achieve with meditation? Not everyone here is working directly for kundalini ascension and the Magnum Opus. Some are working for more efficient spiritual warfare first and foremost, others want specific siddhis. You have to decide what your goals are. The more serious and advanced the goals, the more important is to make your priorities and focus properly. Those who have more light-hearted goals and are just experimenting, and those who belong to the iron and bronze classes of society, can afford to have less focus and to operate at a lower level of power.
To recap and answer your questions more directly:
• Will it still work effectively? Yes, it will.
• Is doing meditations with eyes closed more effective than doing it whit eyes opened? Yes, it is in all cases.