I don’t know what technique the Brennan Center used to account for uncontested races in their report — their methodology section is silent on that — but I’m guessing they do account for these races in some way.
The general technique is called “imputation.” The authors of the efficiency gap discuss the technique they used in their original paper (http://chicagounbound.uchicago.edu/cgi/viewcontent.cgi?article=1946&context=public_law_and_legal_theory).
Here’s a relevant blurb from PP. 27–28:
“For congressional races, we obtained presidential vote share data at the district level, and then ran regressions of vote choice in contested seats on incumbency status and district presidential vote separately for each election year. From this information, we imputed values for uncontested seats. For uncontested Democrats, this procedure resulted in a mean Democratic vote share of 70%, with 90% of values falling between 56% and 87%. For uncontested Republicans, it produced a mean Democratic vote share of 32%, with 90% of values falling between 22% and 43%.”