Should "which percentage" or "what percentage" be used within a sentence?

You should use what.

The "of which" in the text refers to subsets of the 70 (or 130) fish, not the percentages. There is no reason to consider "matching" this usage when asking the subsequent question.

It would only be valid to ask "which percentage" if the text had presented two (or more) percentage values, one of which is the correct answer. In this case, neither percentage specified is the answer.

One would place the commas exactly where they are as cited in the question text. In both cases, "of which X% are goldfish" is a non-restrictive clause (it's still the same tank with that many fish in it, whether the percentage is specified or not). Such clauses are set off with commas, but since the sentence ends after the second such clause, the role of "closing comma" is covered by the full stop.