"Yes, there are bags there."
Translation:Igen, vannak ott táskák.
"Igen, ott táskák vannak" says something like "Yes, it is bags there", "yes, the things that are there are bags". It is emphasizing the bags. Those things are bags, not something else. That place is where you would find bags.
As opposed to "there are bags there".
So, it is a valid sentence but it means something different.
Your other sentence, "Igen, táskák ott vannak", sounds weird to me. But in the right context, it could be okay.
But this is the alternative I can imagine for the above sentence:
"Igen, ott vannak táskák".
This is as neutral as "Igen, vannak ott táskák".