Still, the EEM is on pace to post its first positive year in four, up nearly 8 percent year-to-date after an 18 percent plunge in 2015. The S&P 500 is up about 6.8 percent for 2016 after ending only a touch lower the prior year.
"The market is digesting that change and potential risk of renegotiation of trade deals and rate hikes," USAA's Latif said. From a longer-term perspective, "valuation would tell you in the next 3 to 5 years [emerging markets] is going to be one of the strong performing asset classes."
The MSCI emerging market index had a price-to-earnings ratio of 14.94 at the end of October, versus 22.63 for the MSCI USA index.
Part of the confidence in emerging markets also relies on a view that Trump will have a softer stance on trade as president than during his campaign.
"The U.S. will never, never have the capacity to renegotiate the trade agreements," said Philippe Ithurbide, global head of research, strategy and analysis at Amundi, which has more than $1 trillion in assets under management. "Perhaps we are wrong," he said, but no major changes on trade policy is our "central scenario."
Trump has called for a 45-percent tariff on imports from China and deportation of undocumented immigrants, while threatening to withdraw the United States from the World Trade Organization—an outgrowth of the populism sweeping developed economies.
"Last time we had a surge in protectionism we had a war, massive decline in trade, massive recession worldwide," Ithurbide said. On the small chance that Trump does implement tariffs and anti-immigration policies, he said the U.S. economy would likely fall into "a deep recession" and global growth would slow to 2 percent or less.
On Thursday, Barclays said the strong dollar and potential Trump changes on trade policy contributed to its decision to turn tactically neutral on emerging markets.
But Keith Parker, global equity strategist, also said the firm would look for opportunities to buy dips.
"We continue to believe that [emerging market] equities have the greatest upside potential over the medium term, given relative valuations, potential growth and the relative valuations, potential growth and the relative cyclical position (outside of China)," he said in a note.