"Is there any luggage?" Would be a more direct translation, out of context.

They both work, but using -が implies having rather than -は which is being.

荷物はありますな？

Im pretty confident it is suppose to be Ga than Wa.

Why is にもつをもっていますか？ not acceptable?

(In the same vein that けいたい電話をもっていますか？, or something quite similar to that, is accepted in another exercise for 'Do you have a cellphone'?)

When would you say を instead of は？

Not*

I'm not sure but I think "is there any luggage" would be a more literal translation.