I humbly suggest that Joel misread. I don’t think this is correct.

Let me try to make this clear for you.

ボビーさん 　は　すし　を　たべます。
Bobby will eat sushi.
… would be the answer to…
ボビーさん　が　なに　を　たべますか？
What will Bobby eat?

ボビーさん 　が 　すし　を　たべます。
Bobby will eat sushi.
… would be the answer to…
すし　を　だれ　たべますか？
Who will eat sushi?

First case : you don’t need to emphasize ボビーさん, because the person who asked the question introduced him as the topic using が. What’s important in your reply is the part that actually gives the person the information they want (i.e. that すし is what Bobby will eat). That’s what I guess Koichi means when he says that は emphasizes what comes after.

Second case : the person who asked the question didn’t introduce any topic. A topic is something that is defined and “who” is, in essence, undefined. Besides, Bobby wasn’t mentioned. So you will have to use が to introduce ボビーさん as the topic of your reply. This time, the important part of your answer comes before the particle. They know sushi will be eaten, what they want to know is by whom. That would be ボビーさん.

So, as for your example, there are two possible situations:

-These people weren’t talking about food before.
The person who asks the question has to use が to introduce たべもの as the topic. Once it’s done and until the topic changes, が won’t be needed anymore for たべもの. So は should be used in the answer （and the following sentences）.

-These people were already talking about food.
Since they were already talking about it, たべもの is clearly the topic. が is not needed – it might have been used sooner in the conversation, though – and both persons should use は.

Joel is obviously welcome to correct me if I said anything wrong.

Well, as the name implies, on’yomi reading is how the kanji is supposed to be read (in a sizeable amount of situations). So, unless you’re trying to learn Japanese without actually learning how to read Japanese (which would be bold since 99% of the learning material is text), yes, you have to learn them.

You shouldn’t memorize all of the readings in one go, though. As Koichi advises in his course, you should rather learn the most common reading(s) first and the other ones “in the long run”. But I don’t think you will get to said long run with zero knowledge of on’yomi readings and even if you do, that’ll just be more things to learn when you get there. So I’d suggest you follow Koichi’s advice.

I don’t know anything about Wanikani’s SRS, but if the algorithm is any good, you should quickly get to a point where it’s not annoyingly easy anymore.

As for tips, Textfugu’s mnemonics are pretty good. Better than I thought they would be, actually. Besides that, the secret is that there is no secret: work is what gets you somewhere.

Cheers!