"Are there flowers?"
for reference, if you are bringing up a topic, it should be は (as in questioning), if you are saying something related to your money が makes more sense.
So what you will usually see is 「お金はありますか？」for questions and「お金があります」for facts about yourself as in "I have money". However you can use both が and は in both cases, it just depends of the context and how do you wanna change a topic or not.
As of now it is optional. But from my understanding, certain things that are considered honorable have お before it, such as おさけ、おげんきです、おちゃ、etc.
Both o and wa are optional in colloquial Japanese. But if we have to stick to strict grammar I guess the answer makes sense.
Why is it 'arimasu' here while flowers are animate objects? Shouldn't it be ' imasu' ? Or do you use 'arimasu' because.. the flowers aren't seen as alive?
Plants are usually considered inanimate in Japanese. There's a good discussion of the categories of animacy for Japanese on wikipedia. https://en.wikipedia.org/wiki/Animacy#Japanese
Generally, people and animals are animate, and non-living objects and plants are considered inanimate. (There are exceptions, like robots can go either way depending if you are emphasizing their animate properties or not).