Translation:Are there flowers?
You don't want to put too much emphasis on a question, that's why questions usually have は。You can do it, but then it wouldn't be a generic question anymore and it would depend on the context.
「お花がありますか？」"is flowers what you have?"
「お花はありますか？」"do you have flowers?" "are there flowers? (in this store)"
います and あります is more about animate vs inanimate than living and nonliving
いる is something that moves by itself, so this would mainly be people and animals, but it can also be machines/robots which are non-living but moving. A parked car may be ある but a driving car may be いる. Something that has died would be ある, but depending on the phrasing and the thing that has died, a person or a pet may still take いる. Ghosts and gods/spirits may take either but more likely いる.
Plants are living but they aren't animate, at least not in a visible/meaningful way, so they take ある (It may grow bigger but probably isn't going to make its way to the other side of the room on its own). If someone is particularly fond of a plant though and wishes to personify it they may use いる. Similarly, dolls are inanimate but if they are personified and human-like someone may use いる for them.
This page has some more examples where the distinction gets a bit muddy https://www.imabi.net/aruiru.htm