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)"
No, that still doesn't work because the subject and verb don't agree. "Flowers" is plural, so the plural verb form "are" should be used. You can check this by changing the sentence to a statement rather than a question - "there is flowers" (wrong) vs "there are flowers" (right)