So my question is, would the particle affect the emphasis we want to put on either asking if there ARE Fish inside the pond, or if we are asking how MANY Fish there are in the pond? Or is there no clear answer?
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Go with が. That's what you usually use with いる or ある, because it's a statement, a description ("there is something").
Using は here would be possible in a context where, for instance, you'd want to insist on the fact that it's fish and not something else ("I'm asking if there are fishes in the pond, not birds!")
I would go with は.
If it were an affirmative declarative sentence (肯定平叙文) I'd use が unless a contrastive meaning is intended:
There are many fish in the pond.
This is a statement/description of "There's something".
But in an interrogative sentence (疑問文) as in your question, using は would usually be more natural:
(いけのなかにはさかながたくさんいますか。 would also be natural.)
Here are related questions:
And using は would also be more natural in a negative sentence (否定文):
(To say "There're not so many ~~", あまり～ない would be preferred over たくさん～ない in most contexts, as in いけのなかにさかなはあまりいません。 or いけのなかにはさかながあまりいません。)
The は indicates the scope of negation. For more on this, see:
Yes, the particle affects the emphasis.
は and が can be used to give emphasis by replacing each other.
A sentence where you would normally use は is emphasized by using が, example:
私は学生です。 (I am a student) as opposed to 私が学生です。(I AM the student) >with the second sentence probably being an answer to the question "Who is the student."
The opposite is true, example:
肉が好きです。 (I like meat). 肉は好きです。(I like MEAT, but not other things)
In this case, the normal particle to put before います would be が. If you use は it will emphasize the fishes.
with が: Are there many fishes in the pond? (neutral)
with は: Are there many FISHES in the pond? (only asking about fishes, I don't care about other things that might be in the pond).