It would be enough to build a strong, circumstantial case that could then be aligned with other evidence from other sources. Its not particularly hard for the feds (Mueller) to subpeana phone records and then match it up with other evidence he has by way of other intercepts of the Russians.
Example:
Mueller knows Don Jr. called Trump by way of verifying the phone logs
On a completely seperate intercept, a US intelligence agency picks up a communication between Vesalnitskaya and another Russian where she tells him something to the effect of "We asked Don Jr. about the Magnitsky act support in exchange for providing information on Clinton. He took a break, called his Dad, then came back and said "let's proceed".
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Although Mueller may not have the specific words Trump and Trump Jr said to one another, he would have verification that they spoke and that the Russians understood they had a deal with Trump to proceed.